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Crystal structure of L122V/L132V mutant of nitrophorin 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PEE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.64 24.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.147 α = 90 b = 34.147 β = 90 c = 256.223 γ = 90
Symmetry Space Group P 41 21 2
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 MAR scanner 345 mm plate bent Si-mirror 2003-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 1.1808 APS 14-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 18 84 0.036 11.3 3 12989 12989 18.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 2 49 0.058 10.6 2.4 872
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1PEE 1.9 18 10406 10406 552 84.35 0.14629 0.14629 0.14236 0.22125 0.2727 RANDOM 10.648
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] -0.09 -0.09 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.805 r_dihedral_angle_3_deg 15.985 r_dihedral_angle_4_deg 7.753 r_dihedral_angle_1_deg 7.074 r_scangle_it 4.195 r_scbond_it 3.306 r_mcangle_it 1.956 r_angle_refined_deg 1.814 r_mcbond_it 1.755 r_angle_other_deg 0.916
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.805 r_dihedral_angle_3_deg 15.985 r_dihedral_angle_4_deg 7.753 r_dihedral_angle_1_deg 7.074 r_scangle_it 4.195 r_scbond_it 3.306 r_mcangle_it 1.956 r_angle_refined_deg 1.814 r_mcbond_it 1.755 r_angle_other_deg 0.916 r_mcbond_other 0.35 r_symmetry_hbond_refined 0.213 r_nbd_refined 0.199 r_nbd_other 0.197 r_symmetry_vdw_other 0.193 r_nbtor_refined 0.179 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.126 r_nbtor_other 0.092 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1415 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling