2WVK

Mannosyl-3-phosphoglycerate synthase from Thermus thermophilus HB27 apoprotein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WVL	PDB ENTRY 2WVL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		0.2 M MAGNESIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, 30-35% MPD WITH 600 MM ZNCL2

Crystal Properties
Matthews coefficient	Solvent content
3.6	65.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.456	α = 90
b = 113.456	β = 90
c = 195.982	γ = 90

Symmetry
Space Group	P 41 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 CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.97	45.2	99.4	0.11	19.5	18.9		26864

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	2.97	3.1	96.7		1.27	2.2	18.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2WVL	2.97	42.91	25502	1358	99.57	0.20122	0.19779	0.26636	RANDOM	71.327

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]
-0.17			-0.17		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.463
r_dihedral_angle_3_deg	22.474
r_dihedral_angle_4_deg	20.301
r_dihedral_angle_1_deg	6.693
r_angle_refined_deg	1.731
r_scbond_it	1.175
r_scangle_it	1.09
r_mcangle_it	0.38
r_mcbond_it	0.209
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6076
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing