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Crystal structure of the Cholic acid bound RamR determined with XtaLAB Synergy
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 298 PEG3350, ammonium sulfate, sodium Citrate
Crystal Properties Matthews coefficient Solvent content 2.45 49.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.69 α = 90 b = 53.897 β = 93.06 c = 44.223 γ = 90
Symmetry Space Group C 1 2 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 RIGAKU HyPic-6000HE 2016-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.5406
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 1.55 22.09 99.6 0.034 0.037 0.015 0.999 16.6 4.6 29492
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 1.55 1.58 97.9 0.637 0.772 0.424 0.645 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 (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 3VVY 1.55 22.09 27959 1533 99.49 0.1491 0.1461 0.1461 0.2038 0.2032 RANDOM 35.451
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] -2.54 0.83 2.16 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.726 r_dihedral_angle_4_deg 18.067 r_dihedral_angle_3_deg 16.19 r_dihedral_angle_1_deg 7.804 r_rigid_bond_restr 4.729 r_angle_refined_deg 1.855 r_angle_other_deg 1.631 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.726 r_dihedral_angle_4_deg 18.067 r_dihedral_angle_3_deg 16.19 r_dihedral_angle_1_deg 7.804 r_rigid_bond_restr 4.729 r_angle_refined_deg 1.855 r_angle_other_deg 1.631 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1447 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 34
Software Software Software Name Purpose Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction