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Crystal structure of nitrophorin 4 under pressure of xenon (200 psi)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D2U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 ammonium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.9 34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.196 α = 90 b = 42.461 β = 94.24 c = 52.99 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 100 IMAGE PLATE RIGAKU RAXIS IV osmic mirrors 2001-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 1.45 30.3 96.8 0.04 26.9 3.1 26873 26873 11.8
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) 1.45 1.5 78 0.113 6.8 2.2 2149
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 FOURIER SYNTHESIS THROUGHOUT 1D2U 1.45 30 26873 25510 1362 96.82 0.1447 0.1447 0.14308 0.1501 0.17527 0.1781 RANDOM 10.001
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] -0.12 -0.06 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.321 r_scangle_it 3.79 r_scbond_it 2.484 r_mcangle_it 1.856 r_angle_other_deg 1.83 r_angle_refined_deg 1.808 r_mcbond_it 1.046 r_nbd_other 0.257 r_symmetry_vdw_other 0.242 r_nbd_refined 0.241
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.321 r_scangle_it 3.79 r_scbond_it 2.484 r_mcangle_it 1.856 r_angle_other_deg 1.83 r_angle_refined_deg 1.808 r_mcbond_it 1.046 r_nbd_other 0.257 r_symmetry_vdw_other 0.242 r_nbd_refined 0.241 r_xyhbond_nbd_refined 0.192 r_symmetry_hbond_refined 0.166 r_symmetry_vdw_refined 0.164 r_chiral_restr 0.106 r_nbtor_other 0.088 r_metal_ion_refined 0.024 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1557 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction d*TREK data scaling