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Structure of PcuC from Cereibacter sphaeroides in its apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZK0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.2M NaCitrate
Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 1.92 35.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.1 α = 90 b = 48.1 β = 90 c = 110.66 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 PIXEL DECTRIS EIGER X 16M 2019-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9184 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.05 48 99.6 0.99 17.8 20 61356
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.05 1.08 0.53
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.05 44.113 61262 3064 99.535 0.185 0.184 0.1924 0.2007 0.2057 14.613
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] -0.006 -0.006 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.735 r_dihedral_angle_3_deg 14.779 r_dihedral_angle_2_deg 8.193 r_lrange_it 7.032 r_lrange_other 6.454 r_dihedral_angle_1_deg 6.298 r_scangle_it 4.231 r_scangle_other 4.227 r_mcangle_other 2.891 r_mcangle_it 2.888
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.735 r_dihedral_angle_3_deg 14.779 r_dihedral_angle_2_deg 8.193 r_lrange_it 7.032 r_lrange_other 6.454 r_dihedral_angle_1_deg 6.298 r_scangle_it 4.231 r_scangle_other 4.227 r_mcangle_other 2.891 r_mcangle_it 2.888 r_scbond_it 2.84 r_scbond_other 2.837 r_angle_refined_deg 1.874 r_mcbond_it 1.823 r_mcbond_other 1.802 r_angle_other_deg 0.61 r_symmetry_nbd_refined 0.252 r_xyhbond_nbd_refined 0.248 r_symmetry_xyhbond_nbd_refined 0.243 r_nbd_refined 0.221 r_symmetry_nbd_other 0.212 r_nbd_other 0.208 r_nbtor_refined 0.166 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 889 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing