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Crystal structure of the sclerostin-neutralizing Fab AbD09097
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NH7 PDB entry 3NH7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 20% (w/v) PEG3350, 0.1M HEPES pH 7.5, 10mM zinc chloride
Crystal Properties Matthews coefficient Solvent content 2.08 40.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.193 α = 90 b = 78.495 β = 95.71 c = 59.196 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 IMAGE PLATE RIGAKU RAXIS HTC Rigaku VariMax HF 2012-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.85 20.77 97.9 0.068 10.5 3.66 35146 34389
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 1.85 1.92 80.1 0.3 3.7 2.94 2803
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 PDB entry 3NH7 1.85 20.77 32559 1721 97.49 0.1913 0.1884 0.1906 0.2442 0.2463 RANDOM 29.759
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] 0.88 -1.18 -0.23 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.145 r_dihedral_angle_4_deg 23.529 r_dihedral_angle_3_deg 16.049 r_dihedral_angle_1_deg 7.563 r_mcangle_it 2.517 r_scbond_it 2.291 r_angle_refined_deg 2.006 r_mcbond_it 1.7 r_chiral_restr 0.133 r_bond_refined_d 0.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.145 r_dihedral_angle_4_deg 23.529 r_dihedral_angle_3_deg 16.049 r_dihedral_angle_1_deg 7.563 r_mcangle_it 2.517 r_scbond_it 2.291 r_angle_refined_deg 2.006 r_mcbond_it 1.7 r_chiral_restr 0.133 r_bond_refined_d 0.018 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3346 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection CrystalClear data reduction CrystalClear data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction