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Crystal structure of anti-emmprin antibody 5F6 FAB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NCA PDB entries 1NCA, 1PZ5 experimental model PDB 1PZ5 PDB entries 1NCA, 1PZ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20% PEG 8K, 0.1 M HEPES PH 7.5 CRYO CONDITIONS: 20% PEG 8K, 0.1 M HEPES PH 7.5, 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.61 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.53 α = 90 b = 129.74 β = 109.52 c = 42.39 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 95 CCD RIGAKU SATURN 944 VARIMAX HF 2008-08-08 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 2 15 93.4 0.237 4.8 6.1 30870 30870 -3 30
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 2.07 82 0.419 1.8 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 entries 1NCA, 1PZ5 2 15 29609 29609 1258 89.3 0.19737 0.19737 0.19541 0.1962 0.24274 0.2411 RANDOM 34.2
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] 0.03 0.09 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.099 r_dihedral_angle_4_deg 21.756 r_dihedral_angle_3_deg 16.281 r_scangle_it 9.894 r_scbond_it 8.077 r_dihedral_angle_1_deg 6.622 r_mcangle_it 4.345 r_mcbond_it 2.747 r_angle_refined_deg 1.407 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.099 r_dihedral_angle_4_deg 21.756 r_dihedral_angle_3_deg 16.281 r_scangle_it 9.894 r_scbond_it 8.077 r_dihedral_angle_1_deg 6.622 r_mcangle_it 4.345 r_mcbond_it 2.747 r_angle_refined_deg 1.407 r_nbtor_refined 0.299 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.196 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3328 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 7
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling