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1.11 A Crystal Structure of Apo Nitrophorin 4 From Rhodnius Prolixus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X80 PDB entry 1X80
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 300 ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K
Crystal Properties Matthews coefficient Solvent content 1.93 36.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.47 α = 90 b = 42.816 β = 94.71 c = 52.72 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 CCD ADSC QUANTUM 315 2005-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.11 17.4 93 0.06 0.06 25 2.8 63130 11.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.11 83 0.38 0.38 3.3 2.5
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 FOURIER SYNTHESIS FREE R PDB entry 1X80 1.11 17.4 63130 56059 2984 96.76 0.14803 0.14621 0.1621 0.18266 0.1931 RANDOM 9.595
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] 0.17 -0.13 -0.21 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.234 r_dihedral_angle_3_deg 13.923 r_dihedral_angle_1_deg 7.824 r_dihedral_angle_4_deg 6.408 r_sphericity_free 4.774 r_scangle_it 2.971 r_sphericity_bonded 2.515 r_scbond_it 2.385 r_mcangle_it 1.86 r_angle_other_deg 1.749
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.234 r_dihedral_angle_3_deg 13.923 r_dihedral_angle_1_deg 7.824 r_dihedral_angle_4_deg 6.408 r_sphericity_free 4.774 r_scangle_it 2.971 r_sphericity_bonded 2.515 r_scbond_it 2.385 r_mcangle_it 1.86 r_angle_other_deg 1.749 r_angle_refined_deg 1.664 r_mcbond_it 1.468 r_rigid_bond_restr 1.154 r_mcbond_other 0.543 r_nbd_refined 0.486 r_xyhbond_nbd_other 0.427 r_xyhbond_nbd_refined 0.286 r_nbd_other 0.223 r_nbtor_refined 0.205 r_symmetry_vdw_other 0.205 r_symmetry_hbond_refined 0.188 r_symmetry_vdw_refined 0.183 r_chiral_restr 0.09 r_nbtor_other 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1909 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction