☰ Navigation Tabs
Crystal structure of human ribokinase in P21 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, 25% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.21 44.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.59 α = 90 b = 89.91 β = 98.8 c = 75.14 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 CCD ADSC QUANTUM 315 2010-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
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 2.1 44.96 97.4 0.083 8.7 3.7 34784 29.496
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 2.1 2.15 93.4 0.518 2.2 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 2.1 44.96 32999 1762 97.12 0.17377 0.17149 0.1802 0.21536 0.2199 RANDOM 38.752
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] -0.86 -1.02 0.65 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.077 r_dihedral_angle_4_deg 19.493 r_dihedral_angle_3_deg 13.226 r_dihedral_angle_1_deg 5.763 r_long_range_B_refined 5.713 r_long_range_B_other 5.705 r_scangle_other 3.462 r_mcangle_it 2.358 r_mcangle_other 2.358 r_scbond_it 2.275
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.077 r_dihedral_angle_4_deg 19.493 r_dihedral_angle_3_deg 13.226 r_dihedral_angle_1_deg 5.763 r_long_range_B_refined 5.713 r_long_range_B_other 5.705 r_scangle_other 3.462 r_mcangle_it 2.358 r_mcangle_other 2.358 r_scbond_it 2.275 r_scbond_other 2.274 r_angle_refined_deg 1.735 r_mcbond_it 1.636 r_mcbond_other 1.634 r_angle_other_deg 1.152 r_chiral_restr 0.098 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 4564 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing