4GIB | pdb_00004gib

2.27 Angstrom Crystal Structure of beta-Phosphoglucomutase (pgmB) from Clostridium difficile

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Z4N	PDB entry 1Z4N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	Protein: 7.6mg/mL, 0.25M Sodium cloride, 0.01M Tris-HCl, pH 8.3. Screen: PACT (A3), 0.1M SPG buffer, pH 6.0, 25% (w/v) PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.807	α = 90
b = 51.364	β = 112.04
c = 79.442	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 300 mm CCD	Beryllium lenses	2012-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	2.27	30	99.3	0.097	11.7	3.6	21526	21526		-3	35.4

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)
1	2.27	2.31	97.4		0.439	2.6	3.3	1055

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 1Z4N	2.27	29.92	20343	20343	1099	99.23	0.1962	0.1962	0.1928	0.1951	0.25911	0.2648	RANDOM	26.299

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]
0.28		2.12	-1.64		2.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.724
r_dihedral_angle_3_deg	10.313
r_dihedral_angle_4_deg	10.186
r_scangle_it	4.55
r_scbond_it	3.114
r_dihedral_angle_1_deg	2.381
r_mcangle_it	1.723
r_angle_refined_deg	1.252
r_mcbond_it	0.998
r_angle_other_deg	0.797
r_mcbond_other	0.286
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3546
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	34

Software

Software
Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling