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Structural insights into substrate and cofactor selection by sp2771
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JZ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 293 PEG 5000 MME, Tascimate, HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.44 49.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.928 α = 90 b = 116.963 β = 90 c = 180.604 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 ADSC QUANTUM 315r 2012-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 2.5 50 100 0.072 14.2 32970 2 2
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 2.5 2.54 100
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 3JZ4 2.5 42.12 32967 1755 97.92 0.18002 0.17693 0.1818 0.23658 0.2363 RANDOM 27.58
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] 0.84 -0.2 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.038 r_dihedral_angle_4_deg 19.077 r_dihedral_angle_3_deg 16.851 r_dihedral_angle_1_deg 6.837 r_scangle_it 3.285 r_scbond_it 1.961 r_angle_refined_deg 1.617 r_mcangle_it 1.13 r_angle_other_deg 0.829 r_mcbond_it 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.038 r_dihedral_angle_4_deg 19.077 r_dihedral_angle_3_deg 16.851 r_dihedral_angle_1_deg 6.837 r_scangle_it 3.285 r_scbond_it 1.961 r_angle_refined_deg 1.617 r_mcangle_it 1.13 r_angle_other_deg 0.829 r_mcbond_it 0.65 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.201 r_symmetry_hbond_refined 0.163 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6951 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling