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The structure of the molybdenum cofactor binding protein from the phototrophic bacterium Rippkaea orientalis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IZ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 292 15% (v/v) Pentaerythritol ethoxylate; 0.2 M potassium acetate; 3% (v/v) Jeffamine T-403; 0.1 M MES pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.12 41.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.577 α = 90 b = 72.044 β = 113.333 c = 70.264 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 PIXEL DECTRIS PILATUS 2M-F TOROIDAL FOCUSING MIRRORS 2015-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00003 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.23 64.52 100 0.05279 0.05719 0.02177 1 16.35 6.7 181674 -3 15.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.23 1.274 100 3.026 3.299 1.297 0.193 0.55 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 (All) 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 2IZ6 1.23 64.518 181736 8868 99.999 0.143 0.1418 0.1428 0.1629 0.1628 RANDOM 27.869
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] 0.509 3.035 -3.184 0.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.031 r_dihedral_angle_4_deg 17.84 r_dihedral_angle_3_deg 11.621 r_dihedral_angle_1_deg 5.334 r_rigid_bond_restr 5.013 r_lrange_it 4.121 r_lrange_other 4.023 r_scangle_it 3.917 r_scangle_other 3.917 r_scbond_it 3.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.031 r_dihedral_angle_4_deg 17.84 r_dihedral_angle_3_deg 11.621 r_dihedral_angle_1_deg 5.334 r_rigid_bond_restr 5.013 r_lrange_it 4.121 r_lrange_other 4.023 r_scangle_it 3.917 r_scangle_other 3.917 r_scbond_it 3.335 r_scbond_other 3.334 r_mcangle_other 2.705 r_mcangle_it 2.704 r_mcbond_it 2.266 r_mcbond_other 2.264 r_angle_refined_deg 1.845 r_angle_other_deg 1.691 r_nbd_other 0.282 r_nbd_refined 0.234 r_symmetry_nbd_refined 0.224 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.108 r_symmetry_xyhbond_nbd_refined 0.108 r_ncsr_local_group_6 0.108 r_ncsr_local_group_5 0.107 r_ncsr_local_group_3 0.099 r_ncsr_local_group_2 0.088 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_1 0.081 r_ncsr_local_group_4 0.079 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4774 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 20
Software Software Software Name Purpose XDS data processing Aimless data scaling PHASER phasing SHELXE model building Coot model building REFMAC refinement