3NVS | pdb_00003nvs

1.02 Angstrom resolution crystal structure of 3-phosphoshikimate 1-carboxyvinyltransferase from Vibrio cholerae in complex with shikimate-3-phosphate (partially photolyzed) and glyphosate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1G6S	PDB ENTRY 1G6S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	Protein: 4.0 mGr/mL, 0.25M Sodium cloride, 0.01M Tris-HCl (pH 8.3), 2mM Glyphosate, 1mM Shikimate-3-phosphate; Screen: Classics II (G12), 0.2M Magnesium chloride, 0.1M HEPES (pH 7.5), 25% (w/v) PEG3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.89	35.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.866	α = 90
b = 87.484	β = 105.26
c = 49.994	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Mirrors	2010-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.82648	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.02	15	97.2	0.044	16.3	2.2	178530	178530		-3	6.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.02	1.04	95.5		0.391	2.2	2.2	8695

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1G6S	1.021	14.89	169410	169410	8975	97.17	0.11525	0.11525	0.11406	0.11	0.13767	0.14	RANDOM	8.505

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.39		-0.21	0.2		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.345
r_dihedral_angle_4_deg	16.118
r_dihedral_angle_3_deg	10.672
r_dihedral_angle_1_deg	5.421
r_scangle_it	5.008
r_scbond_it	3.523
r_mcangle_it	2.363
r_mcbond_other	2.137
r_rigid_bond_restr	1.808
r_mcbond_it	1.687

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.345
r_dihedral_angle_4_deg	16.118
r_dihedral_angle_3_deg	10.672
r_dihedral_angle_1_deg	5.421
r_scangle_it	5.008
r_scbond_it	3.523
r_mcangle_it	2.363
r_mcbond_other	2.137
r_rigid_bond_restr	1.808
r_mcbond_it	1.687
r_angle_refined_deg	1.542
r_angle_other_deg	0.979
r_chiral_restr	0.099
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3240
Nucleic Acid Atoms
Solvent Atoms	747
Heterogen Atoms	65

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.