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Bombyx mori lipoprotein 7 - platinum derivative at 1.94 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EFP PDB entry 4EFP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M HEPES buffer, 22% PEG 3350, 200 mM KSCN, 2.0 mM K2PtCl6, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.01 38.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.806 α = 93.17 b = 49.785 β = 94.87 c = 54.958 γ = 102.86
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2010-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 1.071 EMBL/DESY, HAMBURG X12
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 1.94 54.6 94.2 0.068 25.2 3.7 29990 29990 -3
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 1.94 2.01 75 0.153 4.98 2.8
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 (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 4EFP 1.94 54.6 29990 28971 1019 94.08 0.18675 0.18534 0.2008 0.22665 0.2387 RANDOM 20.057
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] 0.02 -1.09 2.04 -1.22 -0.17 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.693 r_dihedral_angle_4_deg 17.178 r_dihedral_angle_3_deg 15.31 r_dihedral_angle_1_deg 6.9 r_scangle_it 3.422 r_scbond_it 2.512 r_angle_refined_deg 1.694 r_mcangle_it 1.426 r_mcbond_it 0.952 r_chiral_restr 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.693 r_dihedral_angle_4_deg 17.178 r_dihedral_angle_3_deg 15.31 r_dihedral_angle_1_deg 6.9 r_scangle_it 3.422 r_scbond_it 2.512 r_angle_refined_deg 1.694 r_mcangle_it 1.426 r_mcbond_it 0.952 r_chiral_restr 0.13 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3836 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 15
Software Software Software Name Purpose HKL-2000 data collection Auto-Rickshaw phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling