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Crystal structure of protein of unknown function DUF402 from Rhodococcus sp. RHA1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 295 0.2M Ammonium acetate, 0.1M Bis-Tris pH 5.5, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.13 42.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.203 α = 90 b = 38.98 β = 107.69 c = 70.721 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 mirrors 2007-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97916 APS 19-ID
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 1.63 40.3 93.1 0.075 14.6 7.9 40684 40684
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 1.63 1.69 52 0.349 2.54 3.9 2264
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.63 40.3 36437 36437 4020 93.46 0.175 0.175 0.171 0.216 0.2503 RANDOM 26.495
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] -2.12 -0.15 1.18 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.861 r_dihedral_angle_4_deg 15.625 r_dihedral_angle_3_deg 13.934 r_dihedral_angle_1_deg 9.531 r_scangle_it 3.879 r_scbond_it 2.618 r_angle_refined_deg 1.596 r_mcangle_it 1.536 r_mcbond_it 0.951 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.861 r_dihedral_angle_4_deg 15.625 r_dihedral_angle_3_deg 13.934 r_dihedral_angle_1_deg 9.531 r_scangle_it 3.879 r_scbond_it 2.618 r_angle_refined_deg 1.596 r_mcangle_it 1.536 r_mcbond_it 0.951 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.179 r_symmetry_hbond_refined 0.177 r_chiral_restr 0.119 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2710 Nucleic Acid Atoms Solvent Atoms 528 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXCD phasing SHELXD phasing MLPHARE phasing RESOLVE phasing ARP/wARP model building