6PBJ | pdb_00006pbj

The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase with Gly190Pro mutation

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NV8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	20 mM BTP, 150 mM NaCl, 0.5 mM TCEP, 0.2 mM PEP, 0.1 mM MnCl2, 2M Li2SO4, 2% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
3.94	68.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 204.251	α = 90
b = 204.251	β = 90
c = 66.551	γ = 120

Symmetry
Space Group	P 32 2 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	ADSC QUANTUM 210r		2014-01-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.95370	Australian Synchrotron	MX1

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	1.9	51.06	99.9	0.131	0.136	0.035	0.995	16.9	14.3		124730

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	1.9	1.93	99.5		1.333	1.429	0.488	0.345		7.4

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3NV8	1.9	36.83	118485	6226	99.82	0.1588	0.1577	0.1799	RANDOM	20.536

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]
2.05			2.05		-4.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.631
r_dihedral_angle_4_deg	18.071
r_dihedral_angle_3_deg	14.063
r_dihedral_angle_1_deg	6.312
r_angle_refined_deg	1.435
r_angle_other_deg	1.358
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.631
r_dihedral_angle_4_deg	18.071
r_dihedral_angle_3_deg	14.063
r_dihedral_angle_1_deg	6.312
r_angle_refined_deg	1.435
r_angle_other_deg	1.358
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6479
Nucleic Acid Atoms
Solvent Atoms	529
Heterogen Atoms	89

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing

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.