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PikC D50N mutant bound to the 10-DML analog with the 3-(N,N-dimethylamino)ethanoate anchoring group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B7S PDB ENTRY 4B7S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 0.2 MGCL, 20% PEG 3350, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.1 41.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.419 α = 90 b = 92.376 β = 90.31 c = 69.251 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARRESEARCH MIRRORS 2013-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 1.89 92.38 89.8 0.11 6.7 3.6 54311 1.5 21.6
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 1.89 1.99 84.1 0.64 1.5 3.7
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 PDB ENTRY 4B7S 1.89 69.25 51511 2753 89.17 0.20047 0.19695 0.1977 0.26721 0.2666 RANDOM 21.193
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] 0.48 -0.23 -1.13 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.354 r_dihedral_angle_4_deg 20.496 r_dihedral_angle_3_deg 14.866 r_dihedral_angle_1_deg 6.385 r_scangle_it 4.102 r_scbond_it 2.85 r_angle_refined_deg 1.928 r_mcangle_it 1.638 r_mcbond_it 1.028 r_chiral_restr 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.354 r_dihedral_angle_4_deg 20.496 r_dihedral_angle_3_deg 14.866 r_dihedral_angle_1_deg 6.385 r_scangle_it 4.102 r_scbond_it 2.85 r_angle_refined_deg 1.928 r_mcangle_it 1.638 r_mcbond_it 1.028 r_chiral_restr 0.135 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_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 6119 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing