3RZI | pdb_00003rzi

The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis cocrystallized and complexed with phenylalanine and tryptophan

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B7O	2B7O, 3KGF
experimental model	PDB	3KGF	2B7O, 3KGF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	20MM BTP, 150MM NACL, 0.5MM TCEP, 0.2MM PEP, 0.1MM MNCL2, 0.1M HEPES, 0.8M NAK PHOSPHATE, pH 8.0, 0.1MM Trp and Phe ligands, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
4.11	70.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 207.56	α = 90
b = 207.56	β = 90
c = 66.977	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	123	IMAGE PLATE	RIGAKU RAXIS IV++	AXCo PX70 capillary optic	2010-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	1.95	31.88	99.2	0.084	8.7	3.96		119335

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	1.95	2.02	95.5		0.442	2.3	2.98	11440

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 (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	2B7O, 3KGF	1.95	31.88	113806	6034	99.49	0.1536	0.1536	0.1529	0.15	0.168	0.17	RANDOM	33.9347

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]
-0.29			-0.29		0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.851
r_dihedral_angle_4_deg	18.167
r_dihedral_angle_3_deg	14.921
r_dihedral_angle_1_deg	7.86
r_scangle_it	6.053
r_scbond_it	4.512
r_mcangle_it	2.855
r_angle_other_deg	2.027
r_mcbond_it	1.998
r_angle_refined_deg	1.962

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.851
r_dihedral_angle_4_deg	18.167
r_dihedral_angle_3_deg	14.921
r_dihedral_angle_1_deg	7.86
r_scangle_it	6.053
r_scbond_it	4.512
r_mcangle_it	2.855
r_angle_other_deg	2.027
r_mcbond_it	1.998
r_angle_refined_deg	1.962
r_mcbond_other	0.506
r_chiral_restr	0.131
r_gen_planes_refined	0.017
r_bond_refined_d	0.016
r_gen_planes_other	0.012
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7011
Nucleic Acid Atoms
Solvent Atoms	495
Heterogen Atoms	136

Software

Software
Software Name	Purpose
d*TREK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction

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.