3D8H | pdb_00003d8h

Crystal structure of phosphoglycerate mutase from Cryptosporidium parvum, cgd7_4270

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XQ9	PDB entry 1XQ9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	273	25% PEG 3350, 0.2 M NH4OAc, 0.1 M Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.248	α = 90
b = 158.365	β = 90
c = 140.249	γ = 90

Symmetry
Space Group	C 2 2 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	RIGAKU RAXIS IV		2008-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.01	50	100	0.075	0.046	9.6	7.2	39125	39125			35.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.01	2.08	100		0.796	0.796	2.32	6.9	3847

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 (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	PDB entry 1XQ9	2.01	40.5	39074	39074	1958	99.74	0.233	0.233	0.231	0.3	0.256	0.32	RANDOM	35.774

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			-0.25		-1.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.578
r_dihedral_angle_4_deg	17.109
r_dihedral_angle_3_deg	14.967
r_dihedral_angle_1_deg	5.92
r_scangle_it	1.504
r_angle_refined_deg	1.141
r_scbond_it	1.02
r_mcangle_it	0.647
r_mcbond_it	0.384
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.578
r_dihedral_angle_4_deg	17.109
r_dihedral_angle_3_deg	14.967
r_dihedral_angle_1_deg	5.92
r_scangle_it	1.504
r_angle_refined_deg	1.141
r_scbond_it	1.02
r_mcangle_it	0.647
r_mcbond_it	0.384
r_nbtor_refined	0.299
r_nbd_refined	0.185
r_symmetry_vdw_refined	0.14
r_xyhbond_nbd_refined	0.129
r_symmetry_hbond_refined	0.127
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3641
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	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.