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Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A4U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 19% PEG3350, 8% ethylene glycol, 0.1 M Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2.18 43.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.063 α = 90 b = 58.765 β = 109.01 c = 119.386 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 95 CCD RAYONIX MX225HE 2011-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
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 50 99.4 0.05 34.9 3.6 46552 46251 -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 2.54 97.8 0.178 8.8 3.3
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 3A4U 2.51 20 43802 2318 98.61 0.195 0.193 0.1969 0.232 0.231 RANDOM 37.97
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] -1.41 0.8 -1.67 2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.767 r_dihedral_angle_4_deg 21.195 r_dihedral_angle_3_deg 16.134 r_dihedral_angle_1_deg 7.103 r_angle_refined_deg 1.533 r_angle_other_deg 1.14 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.767 r_dihedral_angle_4_deg 21.195 r_dihedral_angle_3_deg 16.134 r_dihedral_angle_1_deg 7.103 r_angle_refined_deg 1.533 r_angle_other_deg 1.14 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.007 r_bond_other_d 0.006 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 9252 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing