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Crystal structure of cytidine deaminase from Mycobacterium leprae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MPZ PDB ENTRY 3MPZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 MyleA.00495.a.A1 PS00720 at 66.15 mg/mL against JCSG+ screen condition D6, 0.2 M MgCl2, 0.1 M Tris pH 8.5, 20% PEG 8000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 217493d6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.03 39.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.84 α = 90 b = 79.74 β = 90 c = 104.54 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 ADSC QUANTUM 315r 2011-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97946 ALS 5.0.1
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 2.3 50 99.2 0.081 16.65 6 21771 21604 -3 39.824
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 2.3 2.36 97.5 0.475 3.98 5.6 1584
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 3MPZ 2.3 50 21515 1078 98.84 0.1844 0.1824 0.1901 0.2232 0.1936 RANDOM 35.3068
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] 4.48 -0.71 -3.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.281 r_dihedral_angle_4_deg 21.934 r_dihedral_angle_3_deg 16.209 r_dihedral_angle_1_deg 5.455 r_scangle_it 2.565 r_scbond_it 1.714 r_angle_refined_deg 1.459 r_mcangle_it 0.982 r_mcbond_it 0.544 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.281 r_dihedral_angle_4_deg 21.934 r_dihedral_angle_3_deg 16.209 r_dihedral_angle_1_deg 5.455 r_scangle_it 2.565 r_scbond_it 1.714 r_angle_refined_deg 1.459 r_mcangle_it 0.982 r_mcbond_it 0.544 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3486 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 26
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction BOS data collection XDS data reduction