3FDZ | pdb_00003fdz

Crystal structure of phosphoglyceromutase from burkholderia pseudomallei 1710b with bound 2,3-diphosphoglyceric acid and 3-phosphoglyceric acid

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6	289	30% PEG 600, 5% PEG 1000, 10% GLYCEROL, 100 MM MES PH 6.0, CRYSTALS SOAKED OVERNIGHT WITH 20 MM 3-PHOSPHOGLYCERIC ACID, VAPOR DIFFUSION, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.39	α = 106.03
b = 48.48	β = 91.54
c = 62.09	γ = 107.5

Symmetry
Space Group	P 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	SATURN		2008-09-30		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

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	2.25		93.4	0.071	11.43			20934		-3	29.18

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	2.25	2.31	90.5		0.345	2.6

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.25	19.75	20934	1066		0.187	0.183	0.18	0.256	0.25	RANDOM	23.7

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]
0.6	0.12	-1.14	-0.45	-0.05	-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.445
r_dihedral_angle_3_deg	14.593
r_dihedral_angle_4_deg	13.904
r_dihedral_angle_1_deg	6.698
r_scangle_it	3.013
r_scbond_it	1.923
r_angle_refined_deg	1.526
r_mcangle_it	1.059
r_mcbond_it	0.585
r_chiral_restr	0.091
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3668
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	40

Software

Software
Software Name	Purpose
StructureStudio	data collection
MOLREP	phasing
REFMAC	refinement