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Crystal structure of Biotin carboxylase from E. coli in complex with AMPPNP and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DV2 PDB ENTRY 1DV2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M BIS-TRIS PH 6.5, 0.2M CACL2, 45% MPD
Crystal Properties Matthews coefficient Solvent content 2.17 42.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.704 α = 90 b = 112.251 β = 90 c = 121.769 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 2007-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R
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 2.05 50 99.9 0.08 29.97 7 59125
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 2.05 2.12 100 0.56 4.22 6.7
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DV2 2.05 82.48 56070 2990 99.7 0.192 0.19 0.2056 0.236 RANDOM 23.64
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] 0.46 0.87 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.132 r_dihedral_angle_4_deg 13.74 r_dihedral_angle_3_deg 12.565 r_dihedral_angle_1_deg 5.117 r_scangle_it 1.546 r_angle_refined_deg 1.064 r_scbond_it 1.032 r_angle_other_deg 0.978 r_mcangle_it 0.651 r_mcbond_it 0.603
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.132 r_dihedral_angle_4_deg 13.74 r_dihedral_angle_3_deg 12.565 r_dihedral_angle_1_deg 5.117 r_scangle_it 1.546 r_angle_refined_deg 1.064 r_scbond_it 1.032 r_angle_other_deg 0.978 r_mcangle_it 0.651 r_mcbond_it 0.603 r_symmetry_vdw_other 0.243 r_nbd_other 0.185 r_nbd_refined 0.184 r_symmetry_vdw_refined 0.176 r_nbtor_refined 0.166 r_symmetry_hbond_refined 0.135 r_xyhbond_nbd_refined 0.129 r_nbtor_other 0.08 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 6823 Nucleic Acid Atoms Solvent Atoms 669 Heterogen Atoms 70
Software Software Software Name Purpose SCALEPACK data reduction SCALEPACK data scaling MOLREP phasing REFMAC phasing REFMAC refinement