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b-b' domain fragment of ER-60 (ERp57) under microgravity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H8L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 7 293 50 mM HEPES-NaOH, pH 7.0, 20% PEG3350, 50 mM Ammonium Sulfate, 100 m M NaCl, 0.04% NaN3
Crystal Properties Matthews coefficient Solvent content 2.62 53.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.315 α = 90 b = 62.901 β = 98.64 c = 97.148 γ = 90
Symmetry Space Group P 1 21 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 CCD RAYONIX MX225HE 2011-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.75 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.8 90 99.4 0.029 0.041 0.999 9.31 3.84 82113
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.91 0.297 0.42 0.824
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 2H8L 1.8 47.78 78026 4065 99.57 0.22081 0.21863 0.214 0.26272 0.2567 RANDOM 35.707
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] 7.18 -1.39 -7.97 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.14 r_long_range_B_refined 7.492 r_dihedral_angle_2_deg 7.141 r_dihedral_angle_1_deg 6.828 r_scbond_it 4.618 r_mcangle_it 4.529 r_mcbond_it 3.606 r_angle_refined_deg 2.035 r_chiral_restr 0.141 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.14 r_long_range_B_refined 7.492 r_dihedral_angle_2_deg 7.141 r_dihedral_angle_1_deg 6.828 r_scbond_it 4.618 r_mcangle_it 4.529 r_mcbond_it 3.606 r_angle_refined_deg 2.035 r_chiral_restr 0.141 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_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_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 5673 Nucleic Acid Atoms Solvent Atoms 534 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction XDS data reduction