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Crystal structure of Rv3772 in complex with its substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R5Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 1M succinic acid, HEPES, 1% PEG2000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.56 51.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.414 α = 90 b = 164.46 β = 90 c = 178.515 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 225 mm CCD 2014-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97625 ESRF BM14
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 1.98 50 100 9.6 113605
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 1.98 2.05 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT 4R5Z 1.98 48.21 107832 5680 99.3 0.209 0.208 0.215 0.244 0.248 RANDOM 26.68
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.94 r_dihedral_angle_4_deg 16.098 r_dihedral_angle_3_deg 14.278 r_dihedral_angle_1_deg 5.369 r_angle_refined_deg 1.135 r_angle_other_deg 0.679 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.94 r_dihedral_angle_4_deg 16.098 r_dihedral_angle_3_deg 14.278 r_dihedral_angle_1_deg 5.369 r_angle_refined_deg 1.135 r_angle_other_deg 0.679 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it MAIN-CHAIN ANGLE OTHER ATOMS (A**2) r_scbond_it SIDE-CHAIN BOND OTHER ATOMS (A**2) r_scangle_it SIDE-CHAIN ANGLE OTHER ATOMS (A**2) LONG RANGE B REFINED ATOMS (A**2) LONG RANGE B OTHER ATOMS (A**2) r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10732 Nucleic Acid Atoms Solvent Atoms 908 Heterogen Atoms 168
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling