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L-leucine-binding protein, apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2LBP PDB ENTRY 2LBP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 PEG 5000, SODIUM ACETATE PH 4.6, AMMONIUM SULPHATE, COCL2.
Crystal Properties Matthews coefficient Solvent content 2.3 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.41 α = 90 b = 79.2 β = 133.6 c = 65.18 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 100 2003-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
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 1.53 32.6 95.7 0.046 25.4 3.2 48509
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 1.53 1.56 93.3 0.177 4.9 2.6
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 2LBP 1.53 32.62 46029 2480 100 0.191 0.189 0.2015 0.216 0.2261 RANDOM 18.21
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] -0.86 -0.63 0.8 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.507 r_scangle_it 3.266 r_mcangle_it 2.175 r_scbond_it 1.974 r_angle_refined_deg 1.56 r_mcbond_it 1.35 r_angle_other_deg 0.762 r_symmetry_vdw_refined 0.522 r_nbd_other 0.257 r_nbd_refined 0.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.507 r_scangle_it 3.266 r_mcangle_it 2.175 r_scbond_it 1.974 r_angle_refined_deg 1.56 r_mcbond_it 1.35 r_angle_other_deg 0.762 r_symmetry_vdw_refined 0.522 r_nbd_other 0.257 r_nbd_refined 0.227 r_symmetry_vdw_other 0.22 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.094 r_nbtor_other 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 2596 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing