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Bombyx mori lipoprotein 7 (crystal form II) at 2.50 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, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.1 α = 78.79 b = 71.72 β = 89.98 c = 105.12 γ = 75.79
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 2011-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.949 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 2.5 37 88.8 0.043 13.88 1.8 29885 29884 -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 2.5 2.56 88.8 0.147 4.67 1.6
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 2.5 37 29885 28935 949 88.82 0.2038 0.20112 0.2097 0.28532 0.2859 RANDOM 36.656
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] 1.42 0.61 -0.25 -2.42 0.87 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.889 r_dihedral_angle_3_deg 20.136 r_dihedral_angle_4_deg 19.956 r_dihedral_angle_1_deg 8.391 r_scangle_it 3.847 r_scbond_it 2.734 r_angle_refined_deg 1.983 r_mcangle_it 1.468 r_mcbond_it 0.878 r_chiral_restr 0.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.889 r_dihedral_angle_3_deg 20.136 r_dihedral_angle_4_deg 19.956 r_dihedral_angle_1_deg 8.391 r_scangle_it 3.847 r_scbond_it 2.734 r_angle_refined_deg 1.983 r_mcangle_it 1.468 r_mcbond_it 0.878 r_chiral_restr 0.138 r_bond_refined_d 0.02 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 7667 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 12
Software Software Software Name Purpose XDS data scaling Auto-Rickshaw phasing REFMAC refinement XDS data reduction