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Crystal structure of ERGIC-53/MCFD2, Calcium/Man3-bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WHU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 20% PEG5000 monomethyl ether, 100mM Bis-Tris, 10mM CaCl2, 10mM alpha2-mannotriose, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.95 36.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.257 α = 90 b = 58.212 β = 109.32 c = 55.435 γ = 90
Symmetry Space Group C 1 2 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 315 2013-11-23 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 2.75 50 99.5 0.079 31.1 3.5 8058 8017 -3 57.8
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 2.75 2.8 99.8 0.438 4 3.6 419
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 3WHU 2.75 20 7566 7566 369 99.5 0.2064 0.2026 0.2095 0.2868 0.2877 RANDOM 79.0963
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] -6.36 -2.21 -5.2 9.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.047 r_dihedral_angle_4_deg 24.492 r_dihedral_angle_3_deg 18.512 r_dihedral_angle_1_deg 7.57 r_angle_refined_deg 1.45 r_angle_other_deg 0.756 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.047 r_dihedral_angle_4_deg 24.492 r_dihedral_angle_3_deg 18.512 r_dihedral_angle_1_deg 7.57 r_angle_refined_deg 1.45 r_angle_other_deg 0.756 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2235 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 27
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling