2BLE

Structure of human guanosine monophosphate reductase GMPR1 in complex with GMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EEPPDB ENTRY 1EEP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.1 NA-CACODYLATE PH=6.5 17% PEG10K 0.2 M CA-ACETATE 25% GLYCEROL, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.447.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.78α = 90
b = 117.78β = 90
c = 54.42γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMIRRORS2005-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.94089.10.1227.17.6274312
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9278.70.462.114.04

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1EEP1.94025997140189.10.180.1770.228RANDOM18.71
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]
-1.99-1.993.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.009
r_dihedral_angle_4_deg16.615
r_dihedral_angle_3_deg14.86
r_scangle_it8.631
r_dihedral_angle_1_deg6.353
r_scbond_it6.223
r_mcangle_it3.581
r_mcbond_it2.333
r_angle_refined_deg1.663
r_angle_other_deg0.836
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.009
r_dihedral_angle_4_deg16.615
r_dihedral_angle_3_deg14.86
r_scangle_it8.631
r_dihedral_angle_1_deg6.353
r_scbond_it6.223
r_mcangle_it3.581
r_mcbond_it2.333
r_angle_refined_deg1.663
r_angle_other_deg0.836
r_mcbond_other0.689
r_symmetry_vdw_refined0.269
r_nbd_refined0.216
r_symmetry_vdw_other0.208
r_nbd_other0.186
r_nbtor_refined0.185
r_xyhbond_nbd_refined0.164
r_symmetry_hbond_refined0.125
r_chiral_restr0.096
r_nbtor_other0.087
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 AtomsNumber
Protein Atoms2513
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing