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Crystal structure of NtcA from S. elongatus in apo form B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XKP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294.15 NtcA protein was at 6,1 mg/ml in 50 mM sodium citrate pH 6.5, 0.5 M NaCl, 5 mM magnesium cloride, 50 mM arginine hydrocloride, 50 mM Na L-glutamate. CRYSTALLIZATION SOLUTION: 0,05 M Tris-HCL pH8, 2M NaCl, 2% 2-methyl-2,4-pentanediol,10mM MgCl2, 5%DMSO. CRYO PROTECTANT: 27% 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 3.42 64.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.385 α = 90 b = 96.385 β = 90 c = 126.893 γ = 120
Symmetry Space Group P 64 2 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 CCD MARMOSAIC 225 mm CCD 2010-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9762 ESRF BM14
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 3.3 83.5 100 0.136 4 6.6 5530
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 3.3 3.51 0.419
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.33 48.19 5253 247 99.91 0.22441 0.22198 0.2272 0.27392 0.2736 RANDOM 61.692
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] -0.29 -0.15 -0.29 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.655 r_long_range_B_refined 11.654 r_long_range_B_other 11.649 r_dihedral_angle_2_deg 10.78 r_scangle_other 8.454 r_mcangle_other 7.879 r_mcangle_it 7.868 r_dihedral_angle_1_deg 6.321 r_scbond_it 5.659 r_scbond_other 5.656
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.655 r_long_range_B_refined 11.654 r_long_range_B_other 11.649 r_dihedral_angle_2_deg 10.78 r_scangle_other 8.454 r_mcangle_other 7.879 r_mcangle_it 7.868 r_dihedral_angle_1_deg 6.321 r_scbond_it 5.659 r_scbond_other 5.656 r_mcbond_it 5.125 r_mcbond_other 5.085 r_angle_refined_deg 1.52 r_angle_other_deg 0.506 r_chiral_restr 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1657 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction MOLREP phasing