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The Crystal Structure of Mcbe1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DPM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 0.1 M Citric acid pH 4.0 and 1.0 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.3 46.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.446 α = 90 b = 73.75 β = 90 c = 160.988 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 Bruker Platinum 135 HELIOS MIRRORS 2013-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5419
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 1.9 43.429 100 0.0766 12.8 6.39 50187
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 1.9 2 99.9 0.5786 1.61 4.07
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2DPM 1.9 43.429 50066 2498 99.858 0.208 0.2057 0.2124 0.2436 0.2506 30.158
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] -0.451 1.69 -1.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.765 r_dihedral_angle_4_deg 20.595 r_dihedral_angle_3_deg 15.691 r_lrange_it 7.384 r_lrange_other 7.301 r_dihedral_angle_1_deg 7.079 r_scangle_it 5.155 r_scangle_other 5.154 r_mcangle_it 3.926 r_mcangle_other 3.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.765 r_dihedral_angle_4_deg 20.595 r_dihedral_angle_3_deg 15.691 r_lrange_it 7.384 r_lrange_other 7.301 r_dihedral_angle_1_deg 7.079 r_scangle_it 5.155 r_scangle_other 5.154 r_mcangle_it 3.926 r_mcangle_other 3.926 r_scbond_it 3.289 r_scbond_other 3.289 r_mcbond_it 2.652 r_mcbond_other 2.652 r_angle_refined_deg 1.529 r_angle_other_deg 1.323 r_symmetry_xyhbond_nbd_refined 0.212 r_nbd_other 0.211 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.181 r_symmetry_nbd_other 0.177 r_symmetry_xyhbond_nbd_other 0.155 r_symmetry_nbd_refined 0.146 r_ncsr_local_group_1 0.13 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3928 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement MOLREP phasing PROTEUM PLUS data scaling PROTEUM PLUS data collection PROTEUM PLUS data reduction