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Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VBT PDB ENTRY 2VBT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 35% V/V MPD, 100 MM IMIDAZOLE
Crystal Properties Matthews coefficient Solvent content 3 58.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.845 α = 90 b = 104.845 β = 90 c = 32.802 γ = 90
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 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 1.7 33.15 99.8 0.05 23.1 7.82 20274
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 1.7 1.8 99.4 0.47 4.35 6.3
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 2VBT 1.7 20 18949 997 100 0.163 0.161 0.1662 0.212 0.2158 RANDOM 22.19
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] -0.6 -0.6 1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.208 r_dihedral_angle_3_deg 14.808 r_scangle_it 11.901 r_dihedral_angle_4_deg 11.557 r_scbond_it 8.221 r_dihedral_angle_1_deg 5.712 r_mcangle_it 5.493 r_angle_other_deg 3.826 r_mcbond_it 3.775 r_angle_refined_deg 1.551
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.208 r_dihedral_angle_3_deg 14.808 r_scangle_it 11.901 r_dihedral_angle_4_deg 11.557 r_scbond_it 8.221 r_dihedral_angle_1_deg 5.712 r_mcangle_it 5.493 r_angle_other_deg 3.826 r_mcbond_it 3.775 r_angle_refined_deg 1.551 r_symmetry_vdw_other 0.261 r_nbd_other 0.226 r_nbd_refined 0.188 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.142 r_symmetry_vdw_refined 0.118 r_nbtor_other 0.115 r_symmetry_hbond_refined 0.089 r_chiral_restr 0.074 r_bond_refined_d 0.012 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d 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 1065 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing