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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 6.5 0.1 NA-CACODYLATE PH=6.5 17% PEG10K 0.2 M CA-ACETATE 25% GLYCEROL, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.4 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.78 α = 90 b = 117.78 β = 90 c = 54.42 γ = 90
Symmetry Space Group P 4 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 MARMOSAIC 225 mm CCD MIRRORS 2005-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 1.9 40 89.1 0.12 27.1 7.6 27431 2
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 1.9 2 78.7 0.46 2.11 4.04
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 1.9 40 25997 1401 89.1 0.18 0.177 0.1885 0.228 0.2367 RANDOM 18.71
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 -1.99 3.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.009 r_dihedral_angle_4_deg 16.615 r_dihedral_angle_3_deg 14.86 r_scangle_it 8.631 r_dihedral_angle_1_deg 6.353 r_scbond_it 6.223 r_mcangle_it 3.581 r_mcbond_it 2.333 r_angle_refined_deg 1.663 r_angle_other_deg 0.836
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.009 r_dihedral_angle_4_deg 16.615 r_dihedral_angle_3_deg 14.86 r_scangle_it 8.631 r_dihedral_angle_1_deg 6.353 r_scbond_it 6.223 r_mcangle_it 3.581 r_mcbond_it 2.333 r_angle_refined_deg 1.663 r_angle_other_deg 0.836 r_mcbond_other 0.689 r_symmetry_vdw_refined 0.269 r_nbd_refined 0.216 r_symmetry_vdw_other 0.208 r_nbd_other 0.186 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.164 r_symmetry_hbond_refined 0.125 r_chiral_restr 0.096 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 2513 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing