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Crystal structure of LIMP-2 (space group C2221)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F7B pdb entry 4F7B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 30 %w/v Polyethylene Glycol 8000, 0.2 M Ammonium Sulphate, 0.1 M Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.49 64.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.729 α = 90 b = 95.943 β = 90 c = 217.816 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS 6M 2012-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 2.8 30 92.2 0.18 9 6.6 15620 -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 2.8 2.9 94.6 0.636 2.2 5 1535
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 4F7B 2.82 50 14059 770 89.19 0.22344 0.22069 0.2229 0.2759 0.279 RANDOM 63.812
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] -5.96 -3.73 9.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.736 r_dihedral_angle_3_deg 13.054 r_dihedral_angle_4_deg 12.444 r_dihedral_angle_1_deg 4.923 r_long_range_B_refined 2.205 r_long_range_B_other 2.205 r_mcangle_it 1.258 r_mcangle_other 1.257 r_scangle_other 1.24 r_angle_refined_deg 0.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.736 r_dihedral_angle_3_deg 13.054 r_dihedral_angle_4_deg 12.444 r_dihedral_angle_1_deg 4.923 r_long_range_B_refined 2.205 r_long_range_B_other 2.205 r_mcangle_it 1.258 r_mcangle_other 1.257 r_scangle_other 1.24 r_angle_refined_deg 0.986 r_mcbond_it 0.696 r_mcbond_other 0.696 r_scbond_it 0.692 r_scbond_other 0.692 r_angle_other_deg 0.67 r_chiral_restr 0.054 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3175 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 363
Software Software Software Name Purpose GDA data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling