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Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP and FMN
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 20% W/V PEG 8000, 200 MM SODIUM IODIDE
Crystal Properties Matthews coefficient Solvent content 2.6 52.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.482 α = 90 b = 73.299 β = 90 c = 104.907 γ = 90
Symmetry Space Group P 21 21 21
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 2.4 38.58 98.6 0.13 8.67 5.5 12903
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 2.4 2.55 98.5 0.69 2.25 5.62
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 2.4 20 12202 644 100 0.232 0.227 0.2341 0.323 0.3267 RANDOM 42.39
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] 0.84 2.41 -3.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.186 r_dihedral_angle_3_deg 20.516 r_dihedral_angle_4_deg 14.065 r_dihedral_angle_1_deg 8.057 r_angle_other_deg 4.036 r_scangle_it 2.951 r_scbond_it 1.814 r_angle_refined_deg 1.7 r_mcangle_it 1.406 r_mcbond_it 0.757
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.186 r_dihedral_angle_3_deg 20.516 r_dihedral_angle_4_deg 14.065 r_dihedral_angle_1_deg 8.057 r_angle_other_deg 4.036 r_scangle_it 2.951 r_scbond_it 1.814 r_angle_refined_deg 1.7 r_mcangle_it 1.406 r_mcbond_it 0.757 r_nbd_other 0.23 r_nbd_refined 0.225 r_xyhbond_nbd_refined 0.223 r_symmetry_vdw_other 0.209 r_nbtor_refined 0.196 r_symmetry_vdw_refined 0.184 r_nbtor_other 0.114 r_symmetry_hbond_refined 0.102 r_chiral_restr 0.088 r_bond_refined_d 0.015 r_gen_planes_other 0.007 r_gen_planes_refined 0.005 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 2178 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing