3KD8 | pdb_00003kd8

Cofactor-Independent Phosphoglycerate mutase from Thermoplasma Acidophilum DSM 1728

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	296	0.16M magnesium chloride 0.08M tris HCl, pH 8.5 24% PEG 4000 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.911	α = 90
b = 137.081	β = 90
c = 67.088	γ = 90

Symmetry
Space Group	P 21 21 2

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	double-crystal monochromator Si(111)	2009-08-18	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97880, 0.97904	APS	19-BM

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	2.6	73.92	99.84	0.105	30.75	9.5		25760	3

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)
	2.6	2.62	99.5		0.509	2.923	4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.6	73.92	24352	1305	99.81	0.21145	0.20737	0.2096	0.28782	0.285	RANDOM	33.771

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]
0.16			-2.3		2.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.939
r_dihedral_angle_3_deg	20.488
r_dihedral_angle_4_deg	20.357
r_dihedral_angle_1_deg	7.276
r_scangle_it	4.004
r_scbond_it	2.447
r_angle_refined_deg	1.643
r_mcangle_it	1.524
r_mcbond_it	0.786
r_chiral_restr	0.114

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.939
r_dihedral_angle_3_deg	20.488
r_dihedral_angle_4_deg	20.357
r_dihedral_angle_1_deg	7.276
r_scangle_it	4.004
r_scbond_it	2.447
r_angle_refined_deg	1.643
r_mcangle_it	1.524
r_mcbond_it	0.786
r_chiral_restr	0.114
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5616
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms

Software

Software
Software Name	Purpose
SBC-Collect	data collection
MLPHARE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	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.