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Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP and PO4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VBS PDB ENTRY 2VBS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 40% V/V ETHYLENE GLYCOL, 100 MM PHOSPHATE-CITRATE PH 4.2, 200 MM NH4SO4
Crystal Properties Matthews coefficient Solvent content 5.3 76.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.72 α = 90 b = 77.72 β = 90 c = 106.868 γ = 90
Symmetry Space Group P 43 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 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 2.7 38.32 99.5 0.08 16.57 5.5 9448
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 2.7 2.87 98.1 0.92 2.02 5.6
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 2VBS 2.7 20 8971 453 99.7 0.211 0.209 0.2191 0.266 0.2828 RANDOM 60.53
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] 2.32 2.32 -4.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.962 r_dihedral_angle_3_deg 16.911 r_dihedral_angle_4_deg 8.991 r_dihedral_angle_1_deg 6.337 r_angle_other_deg 3.937 r_scangle_it 2.547 r_mcangle_it 1.738 r_angle_refined_deg 1.476 r_scbond_it 1.464 r_mcbond_it 0.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.962 r_dihedral_angle_3_deg 16.911 r_dihedral_angle_4_deg 8.991 r_dihedral_angle_1_deg 6.337 r_angle_other_deg 3.937 r_scangle_it 2.547 r_mcangle_it 1.738 r_angle_refined_deg 1.476 r_scbond_it 1.464 r_mcbond_it 0.932 r_nbd_other 0.225 r_symmetry_vdw_refined 0.213 r_nbd_refined 0.205 r_nbtor_refined 0.191 r_symmetry_vdw_other 0.16 r_xyhbond_nbd_refined 0.151 r_nbtor_other 0.111 r_chiral_restr 0.079 r_bond_refined_d 0.014 r_gen_planes_other 0.005 r_gen_planes_refined 0.004 r_bond_other_d r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_refined 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 1105 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing