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Muramidase domain of SpmX from Asticaccaulis excentricus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ANX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293.15 0.1 M Tris-HCl pH 8.5
0.2 M MgCl2
12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.82 56.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.44 α = 90 b = 100.44 β = 90 c = 96.62 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 273 PIXEL DECTRIS PILATUS3 2M 2015-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965000 ESRF MASSIF-1
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 44.56 95.1 0.02 33.99 3.3 42611 44.4
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 2.01 95 0.436 3.1 3.4
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 2ANX 1.9 44.56 38321 4288 95.15 0.21594 0.21141 0.2249 0.25594 0.2668 RANDOM 41.72
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] 0.38 0.19 0.38 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.681 r_dihedral_angle_4_deg 22.388 r_dihedral_angle_3_deg 14.587 r_long_range_B_other 8.596 r_long_range_B_refined 8.584 r_scangle_other 7.924 r_scbond_it 5.927 r_scbond_other 5.926 r_dihedral_angle_1_deg 5.53 r_mcangle_it 5.471
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.681 r_dihedral_angle_4_deg 22.388 r_dihedral_angle_3_deg 14.587 r_long_range_B_other 8.596 r_long_range_B_refined 8.584 r_scangle_other 7.924 r_scbond_it 5.927 r_scbond_other 5.926 r_dihedral_angle_1_deg 5.53 r_mcangle_it 5.471 r_mcangle_other 5.47 r_mcbond_it 4.522 r_mcbond_other 4.519 r_angle_refined_deg 1.182 r_angle_other_deg 0.943 r_chiral_restr 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3484 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing