☰ Navigation Tabs
Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-free form
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 7 293 1.2 M sodium malonate, 0.5% (v/v) Jeffamine ED-2001, 50 mM Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.17 43.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.924 α = 90 b = 116.93 β = 120.13 c = 58.065 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 ADSC QUANTUM 315r 2013-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00000 Photon Factory BL-5A
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 1.6 50 98.9 0.059 39.2 3.7 88266 87258 -3 19.58
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 1.6 1.63 100 0.466 3.4 3.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3A4U 1.6 20 82482 4370 98.83 0.181 0.18 0.199 0.2079 RANDOM 30.3
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] 1.2 0.42 -1.74 0.03
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.787 r_long_range_B_other 5.688 r_scangle_other 4.746 r_mcangle_it 3.334 r_mcangle_other 3.334 r_scbond_it 3.013 r_scbond_other 3.012 r_mcbond_it 2.267 r_mcbond_other 2.26 r_angle_refined_deg 1.437
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.787 r_long_range_B_other 5.688 r_scangle_other 4.746 r_mcangle_it 3.334 r_mcangle_other 3.334 r_scbond_it 3.013 r_scbond_other 3.012 r_mcbond_it 2.267 r_mcbond_other 2.26 r_angle_refined_deg 1.437 r_angle_other_deg 0.843 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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 4062 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing