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Crystal structure of human endogenous retrovirus HERV-FRD envelope protein (syncitin-2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MOF PDB ENTRY 1MOF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 292 Sodium Chloride, Sodium Acetate tri-hydrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.275 45.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.404 α = 90 b = 90.404 β = 90 c = 38.654 γ = 90
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 MARRESEARCH mirrors 2004-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.95375 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.53 50 94.9 22623 -3 21.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.53 1.58 75.1
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 (All) 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 1MOF 1.6 31.96 23835 19988 1998 96 0.262 0.248 0.248 0.2475 0.262 0.2625 RANDOM 29.8
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] -7.44 -7.44 14.87
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.2 c_scangle_it 3.03 c_scbond_it 2.02 c_mcangle_it 1.94 c_mcbond_it 1.19 c_angle_deg 1.1 c_improper_angle_d 0.57 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.2 c_scangle_it 3.03 c_scbond_it 2.02 c_mcangle_it 1.94 c_mcbond_it 1.19 c_angle_deg 1.1 c_improper_angle_d 0.57 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1198 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 1
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing