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Complement factor B in complex with (S)-5,7-Dimethyl-4-((2-phenylpiperidin-1-yl)methyl)-1H-indole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DLE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 25% PEG3350, 0.1M HEPES PH 7.5, 5 mM inhibitor
Crystal Properties Matthews coefficient Solvent content 2.46 50.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.652 α = 90 b = 97.487 β = 100.465 c = 61.975 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 2012-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.29 60.92 99.1 0.102 0.121 12.22 3.4 28558
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.36 98.1 0.38 0.45 4.16
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1DLE 2.29 48.743 28552 1428 99.153 0.205 0.2023 0.2022 0.2539 0.2539 24.576
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] -0.018 -0.072 0.076 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.667 r_dihedral_angle_3_deg 18.529 r_dihedral_angle_4_deg 18.513 r_lrange_it 6.7 r_dihedral_angle_1_deg 6.6 r_scangle_it 4.432 r_mcangle_it 3.291 r_scbond_it 2.86 r_mcbond_it 1.993 r_angle_refined_deg 1.497
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.667 r_dihedral_angle_3_deg 18.529 r_dihedral_angle_4_deg 18.513 r_lrange_it 6.7 r_dihedral_angle_1_deg 6.6 r_scangle_it 4.432 r_mcangle_it 3.291 r_scbond_it 2.86 r_mcbond_it 1.993 r_angle_refined_deg 1.497 r_nbtor_refined 0.313 r_symmetry_nbd_refined 0.224 r_nbd_refined 0.203 r_symmetry_xyhbond_nbd_refined 0.155 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.118 r_ncsr_local_group_1 0.108 r_symmetry_metal_ion_refined 0.047 r_metal_ion_refined 0.013 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4402 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing