2BWG

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
116% PEG3350 0.30 M K3CIT
Crystal Properties
Matthews coefficientSolvent content
2.242.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.312α = 90
b = 114.418β = 102.74
c = 115.129γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATE2005-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E

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
12.419.990.10.127.142.83154258
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)
12.42.580.80.3722.27

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 1EEP2.44046582252090.10.1990.1960.245RANDOM19.81
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]
3.1-1.74-1.68-2.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.271
r_dihedral_angle_4_deg21.286
r_dihedral_angle_3_deg17.003
r_dihedral_angle_1_deg5.767
r_scangle_it5.509
r_scbond_it3.63
r_mcangle_it2.054
r_angle_refined_deg1.352
r_mcbond_it1.104
r_angle_other_deg0.802
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.271
r_dihedral_angle_4_deg21.286
r_dihedral_angle_3_deg17.003
r_dihedral_angle_1_deg5.767
r_scangle_it5.509
r_scbond_it3.63
r_mcangle_it2.054
r_angle_refined_deg1.352
r_mcbond_it1.104
r_angle_other_deg0.802
r_symmetry_vdw_other0.194
r_nbd_refined0.191
r_nbd_other0.182
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.174
r_symmetry_vdw_refined0.13
r_nbtor_other0.085
r_symmetry_hbond_refined0.085
r_chiral_restr0.071
r_bond_refined_d0.013
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
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_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 AtomsNumber
Protein Atoms9820
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing