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Crystal structure of the Gefitinib Intermediate 1 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 2.51 51.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.513 α = 74.64 b = 54.792 β = 81.94 c = 92.224 γ = 89.98
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 2.2 18.44 99.3 0.106 0.123 0.062 0.992 6.2 3.4 40974
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 2.2 2.27 98.9 0.587 0.76 0.476 0.565 2.3
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 2.2 18.44 38659 2033 98.59 0.2236 0.2196 0.2257 0.2992 0.3022 RANDOM 57.627
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] 0.07 0.16 -0.64 -1.78 -1.17 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.43 r_dihedral_angle_4_deg 22.584 r_dihedral_angle_3_deg 21.509 r_dihedral_angle_1_deg 6.58 r_angle_refined_deg 1.566 r_angle_other_deg 1.321 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.43 r_dihedral_angle_4_deg 22.584 r_dihedral_angle_3_deg 21.509 r_dihedral_angle_1_deg 6.58 r_angle_refined_deg 1.566 r_angle_other_deg 1.321 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.008 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5848 Nucleic Acid Atoms Solvent Atoms 662 Heterogen Atoms 113
Software Software Software Name Purpose Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction