3M8W | pdb_00003m8w

Phosphopentomutase from Bacillus cereus

X-RAY DIFFRACTION

---

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.238	α = 90
b = 76.552	β = 108.89
c = 106.561	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	100	CCD	MARMOSAIC 225 mm CCD			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	1.85	45.7	98.6	0.08	13.3	3.1		116902		2.5	19.1

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)
	1.85	1.92	99.1		0.369	3	2.9	11723

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		THROUGHOUT	1.85	20	116800	5847	100	0.1582	0.1568	0.1588	0.1857	0.1863	RANDOM	31.2195

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]
1.52		-1.27	-1.04		-1.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.479
r_dihedral_angle_4_deg	15.005
r_dihedral_angle_3_deg	12.589
r_dihedral_angle_1_deg	5.441
r_scangle_it	2.127
r_scbond_it	1.238
r_angle_refined_deg	1.08
r_mcangle_it	0.674
r_mcbond_it	0.346
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9196
Nucleic Acid Atoms
Solvent Atoms	948
Heterogen Atoms	38

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling