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Human guanine deaminase (guaD) in complex with zinc and its product Xanthine.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I9U PDB ENTRY 2I9U
Crystallization Crystal Properties Matthews coefficient Solvent content 2.65 53.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.735 α = 90 b = 85.713 β = 116.49 c = 78.96 γ = 90
Symmetry Space Group C 1 2 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 CCD MARRESEARCH 2006-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
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 2.3 20 99.8 0.1 13.3 3.7 24361
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 2.3 2.42 100 0.51 2.5 3.7
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 2I9U 2.3 30 23120 1241 99.9 0.172 0.169 0.1732 0.222 0.221 RANDOM 27.93
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] -0.99 0.25 -1.73 2.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.641 r_dihedral_angle_3_deg 17.02 r_dihedral_angle_4_deg 14.095 r_dihedral_angle_1_deg 6.592 r_scangle_it 2.93 r_scbond_it 2.151 r_mcangle_it 1.508 r_angle_refined_deg 1.366 r_mcbond_it 1.164 r_angle_other_deg 0.953
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.641 r_dihedral_angle_3_deg 17.02 r_dihedral_angle_4_deg 14.095 r_dihedral_angle_1_deg 6.592 r_scangle_it 2.93 r_scbond_it 2.151 r_mcangle_it 1.508 r_angle_refined_deg 1.366 r_mcbond_it 1.164 r_angle_other_deg 0.953 r_symmetry_vdw_other 0.261 r_nbd_refined 0.194 r_nbd_other 0.192 r_nbtor_refined 0.178 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.149 r_nbtor_other 0.087 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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_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 3521 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing