4I9F | pdb_00004i9f

Crystal structure of glycerol phosphate phosphatase Rv1692 from Mycobacterium tuberculosis in complex with calcium

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	HEPES (50 mM) pH 7.5 PEG 4000 (10% w/v), Sodium citrate trihydrate (40 mM), and CaCl2 (100 mM), VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.814	α = 90
b = 70.318	β = 95.56
c = 97.099	γ = 90

Symmetry
Space Group	C 1 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	MARMOSAIC 300 mm CCD		2012-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.0	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	50	98.5			31079	30613		2

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 (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 3PDW	2.21	40	31079	30613	1640	97.27	0.19373	0.19102	0.19	0.24284	0.24	RANDOM	38.093

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]
1.8		-0.26			-1.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.676
r_dihedral_angle_4_deg	19.503
r_dihedral_angle_3_deg	17.584
r_dihedral_angle_1_deg	5.387
r_angle_refined_deg	1.146
r_angle_other_deg	0.765
r_chiral_restr	0.061
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4997
Nucleic Acid Atoms
Solvent Atoms	331
Heterogen Atoms	4

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.