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Crystal structure of 13D9 FAB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MAM FAB FROM YST9.1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 PEG 10000, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.93 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.75 α = 90 b = 100.28 β = 90 c = 132.19 γ = 90
Symmetry Space Group P 21 21 21
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 OSMIC BLUE MIRRORS 2006-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002 1.54
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 2.06 20 88.4 0.058 12 4.67 31114
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 2.06 2.13 91.8 0.293 3.8 4.39
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 FAB FROM YST9.1 2.06 20 31104 1556 88.4 0.217 0.213 0.2114 0.286 0.2829 RANDOM 32.55
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] 2.74 -1.31 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.963 r_dihedral_angle_4_deg 25.174 r_dihedral_angle_3_deg 19.082 r_dihedral_angle_1_deg 7.613 r_scangle_it 4.004 r_scbond_it 2.89 r_angle_refined_deg 1.985 r_mcangle_it 1.954 r_mcbond_it 1.228 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.963 r_dihedral_angle_4_deg 25.174 r_dihedral_angle_3_deg 19.082 r_dihedral_angle_1_deg 7.613 r_scangle_it 4.004 r_scbond_it 2.89 r_angle_refined_deg 1.985 r_mcangle_it 1.954 r_mcbond_it 1.228 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.235 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.166 r_symmetry_vdw_refined 0.156 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3315 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement d*TREK data reduction d*TREK data scaling