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Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with PO4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P3M PDB ENTRY 2P3M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 2M NH4SO4
Crystal Properties Matthews coefficient Solvent content 5.3 76.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.7 α = 90 b = 77.7 β = 90 c = 107.07 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 3 19.99 99.3 0.13 8.43 4.28 6951
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 3 3.2 100 0.33 4.39 4.43
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 2P3M 3 19.99 6650 334 99.8 0.232 0.23 0.2397 0.282 0.2807 RANDOM 49.89
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] 4.19 4.19 -8.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.139 r_dihedral_angle_3_deg 20.764 r_dihedral_angle_4_deg 17.43 r_dihedral_angle_1_deg 8.289 r_angle_other_deg 4.008 r_scangle_it 1.735 r_angle_refined_deg 1.538 r_mcangle_it 1.139 r_scbond_it 1.056 r_mcbond_it 0.624
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.139 r_dihedral_angle_3_deg 20.764 r_dihedral_angle_4_deg 17.43 r_dihedral_angle_1_deg 8.289 r_angle_other_deg 4.008 r_scangle_it 1.735 r_angle_refined_deg 1.538 r_mcangle_it 1.139 r_scbond_it 1.056 r_mcbond_it 0.624 r_symmetry_vdw_refined 0.365 r_nbd_other 0.229 r_nbd_refined 0.227 r_symmetry_vdw_other 0.207 r_nbtor_refined 0.195 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.156 r_nbtor_other 0.116 r_chiral_restr 0.077 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 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 1056 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing