3OT9 | pdb_00003ot9

Phosphopentomutase from Bacillus cereus bound to glucose-1,6-bisphosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3M8W	PDB ENTRY 3M8W

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.871	α = 90
b = 76.582	β = 108.73
c = 107.051	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.979	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.75	50	94	0.053	23.7			141561	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.75	1.81	69.6		0.298	2.8	2.5

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3M8W	1.75	50	126882	6361	94.19	0.1636	0.1623	0.1641	0.1898	0.1917	RANDOM	26.9567

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]
1.05		-0.64	-0.99		-0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.48
r_dihedral_angle_4_deg	13.981
r_dihedral_angle_3_deg	13.031
r_dihedral_angle_1_deg	5.408
r_scangle_it	2.017
r_scbond_it	1.185
r_angle_refined_deg	1.076
r_mcangle_it	0.611
r_mcbond_it	0.31
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9188
Nucleic Acid Atoms
Solvent Atoms	1095
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction