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Human epidermal fatty acid-binding protein (FABP5) in complex with the inhibitor BMS-309413
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B56 PDB ENTRY 1B56
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.32 M SODIUM CITRATE, 0.1 M HEPES PH 7.0, SATURATED WITH RESPECT TO BMS-309403, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K. CRYOPROTECTION: 28% GLYCEROL IN MOTHER LIQUOR.
Crystal Properties Matthews coefficient Solvent content 2.6 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.67 α = 90 b = 104.67 β = 90 c = 58.65 γ = 90
Symmetry Space Group P 4 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 PIXEL DECTRIS PILATUS 6M 2011-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 NSLS X25
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 2.75 20 99.9 0.06 35.6 12.4 8919 -3 72.7
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 2.75 2.85 100 0.6 4.7 12.9
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 PDB ENTRY 1B56 2.75 20 8446 444 99.93 0.20739 0.20503 0.25195 0.2138 RANDOM 55.217
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] 0.04 0.04 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.217 r_dihedral_angle_4_deg 21.123 r_dihedral_angle_3_deg 18.278 r_dihedral_angle_1_deg 6.613 r_scangle_it 2.148 r_angle_refined_deg 1.45 r_scbond_it 1.277 r_mcangle_it 0.739 r_mcbond_it 0.36 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.217 r_dihedral_angle_4_deg 21.123 r_dihedral_angle_3_deg 18.278 r_dihedral_angle_1_deg 6.613 r_scangle_it 2.148 r_angle_refined_deg 1.45 r_scbond_it 1.277 r_mcangle_it 0.739 r_mcbond_it 0.36 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2101 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing