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Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D9R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.1 M sodium cacodylate pH 6.5, 1 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 4.35 71.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.843 α = 90 b = 180.843 β = 90 c = 304.189 γ = 90
Symmetry Space Group P 41 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 CCD ADSC QUANTUM 315 2014-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00003 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.95 50 99.9 0.135 7 7.2 106295 55.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.06 99.8 0.633 6.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4D9R 2.95 47.24 105651 1050 99.36 0.218 0.2175 0.2652 0.22 RANDOM 53.17
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] -6.6529 -6.6529 13.3058
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.53 t_omega_torsion 3.13 t_angle_deg 1.22 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.53 t_omega_torsion 3.13 t_angle_deg 1.22 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19699 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 78
Software Software Software Name Purpose HKL-2000 data scaling BUSTER refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing