3R77 | pdb_00003r77

Crystal structure of the D38A mutant of isochorismatase PhzD from Pseudomonas fluorescens 2-79 in complex with 2-amino-2-desoxyisochorismate ADIC

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.1 M Na-cacodylate, 0.2 M Na-acetate, 25% (w/v) PEG 4000, soaking with 1 mM ADIC for 60 minutes, pH 6.5, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.48	α = 90
b = 72.1	β = 90
c = 78.94	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2010-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.542

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	1.9	49.653	97.7	0.04	18.7			31346		-3	20.851

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	1.9	2	98.2		0.219	4.92

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	1.9	20	31334	1586	99.69	0.1451	0.1426	0.15	0.1918	0.2	RANDOM	27.3776

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]
0.21			-0.4		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.516
r_dihedral_angle_4_deg	19.657
r_dihedral_angle_3_deg	12.371
r_dihedral_angle_1_deg	6.258
r_scangle_it	4.203
r_scbond_it	2.833
r_angle_refined_deg	1.904
r_mcangle_it	1.666
r_mcbond_it	1.051
r_angle_other_deg	0.973

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.516
r_dihedral_angle_4_deg	19.657
r_dihedral_angle_3_deg	12.371
r_dihedral_angle_1_deg	6.258
r_scangle_it	4.203
r_scbond_it	2.833
r_angle_refined_deg	1.904
r_mcangle_it	1.666
r_mcbond_it	1.051
r_angle_other_deg	0.973
r_mcbond_other	0.393
r_chiral_restr	0.12
r_bond_refined_d	0.025
r_gen_planes_refined	0.016
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3197
Nucleic Acid Atoms
Solvent Atoms	454
Heterogen Atoms	36

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.