X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GVXPDB ENTRY 1GVX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.92940.1 M sodium acetate, 63% saturated ammonium sulfate, 3 mg/ml enzyme, 2 mM inhibitor (dissolved initially in DMSO), pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K
Crystal Properties
Matthews coefficientSolvent content
2.3547.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.62α = 90
b = 72.787β = 108.54
c = 45.113γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6MMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I021.0435DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.3528.3298.20.0470.04714.83.3696226962211.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.3884.10.5710.5712.12.34381

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1GVX1.3527.727084366078357698.420.12520.12310.1649RANDOM16.182
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]
0.06-0.03-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free42.192
r_dihedral_angle_2_deg30.028
r_dihedral_angle_4_deg23.079
r_sphericity_bonded12.406
r_dihedral_angle_3_deg11.02
r_dihedral_angle_1_deg6.5
r_rigid_bond_restr5.698
r_long_range_B_refined5.363
r_long_range_B_other5.351
r_scangle_other4.011
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free42.192
r_dihedral_angle_2_deg30.028
r_dihedral_angle_4_deg23.079
r_sphericity_bonded12.406
r_dihedral_angle_3_deg11.02
r_dihedral_angle_1_deg6.5
r_rigid_bond_restr5.698
r_long_range_B_refined5.363
r_long_range_B_other5.351
r_scangle_other4.011
r_scbond_it3.814
r_scbond_other3.808
r_mcangle_other2.472
r_mcangle_it2.466
r_angle_refined_deg2.112
r_mcbond_it2.059
r_mcbond_other1.952
r_angle_other_deg1.018
r_chiral_restr0.129
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_bond_other_d0.004
r_gen_planes_other0.002
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2461
Nucleic Acid Atoms
Solvent Atoms335
Heterogen Atoms51

Software

Software
Software NamePurpose
GDAdata collection
FFTmodel building
REFMACrefinement
XDSdata reduction
SCALAdata scaling
FFTphasing