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The crystal structure of YcgJ protein from Bacillus subitilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XXL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 2.4M Am Sulfate, 0.1M Na Citrate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.9 57.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.899 α = 90 b = 73.639 β = 90 c = 245.742 γ = 90
Symmetry Space Group C 2 2 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 4 2004-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A .979 NSLS X4A
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 2.9 20 94.6 13553 13553 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.9 3 96.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1XXL 2.91 20 -3 13505 13505 678 94.16 0.19686 0.19686 0.19234 0.1985 0.28257 0.2886 RANDOM 27.327
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] 4.69 -0.67 -4.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.949 r_dihedral_angle_3_deg 20.478 r_dihedral_angle_4_deg 17.289 r_dihedral_angle_1_deg 6.822 r_scangle_it 2.343 r_angle_refined_deg 1.648 r_scbond_it 1.509 r_mcangle_it 1.019 r_angle_other_deg 0.921 r_mcbond_it 0.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.949 r_dihedral_angle_3_deg 20.478 r_dihedral_angle_4_deg 17.289 r_dihedral_angle_1_deg 6.822 r_scangle_it 2.343 r_angle_refined_deg 1.648 r_scbond_it 1.509 r_mcangle_it 1.019 r_angle_other_deg 0.921 r_mcbond_it 0.805 r_symmetry_vdw_other 0.258 r_nbd_refined 0.247 r_xyhbond_nbd_refined 0.219 r_nbd_other 0.216 r_symmetry_vdw_refined 0.202 r_nbtor_refined 0.2 r_symmetry_hbond_refined 0.184 r_mcbond_other 0.109 r_xyhbond_nbd_other 0.108 r_nbtor_other 0.095 r_chiral_restr 0.082 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3722 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing