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Crystal structure of human ribokinase in complex with AMPPCP in C2 spacegroup
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FV7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 0.1M sodium HEPES, 10% PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.08 60.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.557 α = 90 b = 72.943 β = 114.81 c = 91.864 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 ADSC QUANTUM 4 2010-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12B 1.1 NSLS X12B
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 50 99.6 0.051 18.464 3.6 67611 -3
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 1.93 100 0.429 2.875 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 2FV7 1.9 50 64182 3427 99.15 0.15125 0.14934 0.1617 0.18766 0.1979 RANDOM 36.267
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] 0.62 -0.11 1.16 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.016 r_dihedral_angle_4_deg 21.558 r_dihedral_angle_3_deg 13.136 r_long_range_B_refined 7.585 r_long_range_B_other 7.585 r_dihedral_angle_1_deg 6.011 r_scangle_other 4.244 r_scbond_it 2.823 r_scbond_other 2.823 r_angle_refined_deg 2.435
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.016 r_dihedral_angle_4_deg 21.558 r_dihedral_angle_3_deg 13.136 r_long_range_B_refined 7.585 r_long_range_B_other 7.585 r_dihedral_angle_1_deg 6.011 r_scangle_other 4.244 r_scbond_it 2.823 r_scbond_other 2.823 r_angle_refined_deg 2.435 r_mcangle_it 2.307 r_mcangle_other 2.307 r_angle_other_deg 1.817 r_mcbond_it 1.71 r_mcbond_other 1.71 r_chiral_restr 0.154 r_bond_refined_d 0.028 r_gen_planes_refined 0.015 r_bond_other_d 0.012 r_gen_planes_other 0.008 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4651 Nucleic Acid Atoms Solvent Atoms 508 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing