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Structure of human guanosine monophosphate reductase GMPR1 in complex with GMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EEP PDB ENTRY 1EEP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 16% PEG3350 0.30 M K3CIT
Crystal Properties Matthews coefficient Solvent content 2.2 42.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.312 α = 90 b = 114.418 β = 102.74 c = 115.129 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE RIGAKU IMAGE PLATE 2005-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E
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 2.4 19.9 90.1 0.12 7.14 2.83 154258
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 2.4 2.5 80.8 0.37 2 2.27
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1EEP 2.4 40 46582 2520 90.1 0.199 0.196 0.2058 0.245 0.252 RANDOM 19.81
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.271 r_dihedral_angle_4_deg 21.286 r_dihedral_angle_3_deg 17.003 r_dihedral_angle_1_deg 5.767 r_scangle_it 5.509 r_scbond_it 3.63 r_mcangle_it 2.054 r_angle_refined_deg 1.352 r_mcbond_it 1.104 r_angle_other_deg 0.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.271 r_dihedral_angle_4_deg 21.286 r_dihedral_angle_3_deg 17.003 r_dihedral_angle_1_deg 5.767 r_scangle_it 5.509 r_scbond_it 3.63 r_mcangle_it 2.054 r_angle_refined_deg 1.352 r_mcbond_it 1.104 r_angle_other_deg 0.802 r_symmetry_vdw_other 0.194 r_nbd_refined 0.191 r_nbd_other 0.182 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.174 r_symmetry_vdw_refined 0.13 r_nbtor_other 0.085 r_symmetry_hbond_refined 0.085 r_chiral_restr 0.071 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 9820 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing