6LLA | pdb_00006lla

Crystal structure of Providencia alcalifaciens 3-dehydroquinate synthase (DHQS) in complex with Mg2+ and NAD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OKF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	10 mM Bis Tris Propane (pH 7.0) buffer, 200 mM MgCl2 and 28% polyethylene glycol 4000

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.39	α = 90
b = 59.92	β = 93.95
c = 143.8	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	PIXEL	DECTRIS PILATUS 6M		2017-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9762	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.87	143.46	98.9	0.05	0.07	0.05	0.997	11.4	3		123349

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.87	1.91			0.45	0.55	0.38	0.81	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	3OKF	1.88	143.46	117334	6015	98.9	0.1765	0.1734	0.18	0.2381	0.24	RANDOM	40.942

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]
-0.09		0.56	0.35		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.815
r_sphericity_bonded	23.495
r_sphericity_free	23.24
r_dihedral_angle_4_deg	17.001
r_dihedral_angle_3_deg	14.891
r_rigid_bond_restr	7.942
r_dihedral_angle_1_deg	6.151
r_angle_refined_deg	1.913
r_angle_other_deg	1.154
r_chiral_restr	0.128

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.815
r_sphericity_bonded	23.495
r_sphericity_free	23.24
r_dihedral_angle_4_deg	17.001
r_dihedral_angle_3_deg	14.891
r_rigid_bond_restr	7.942
r_dihedral_angle_1_deg	6.151
r_angle_refined_deg	1.913
r_angle_other_deg	1.154
r_chiral_restr	0.128
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10917
Nucleic Acid Atoms
Solvent Atoms	1094
Heterogen Atoms	367

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
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.