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Crystal structure of calG3 from Micromonospora echinospora determined in space group P2(1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D0Q PDB entry 3D0Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 Protein solution (10 mg/mL protein, 0.050 M Sodium chloride, 0.010 M Tris-HCl pH 7.5) mixed in a 1:1 ratio with the Well solution (25% PEG 1500). Cryoprotected in FOMBLIN MW2500, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.06 40.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.44 α = 90 b = 97.677 β = 90.62 c = 63.046 γ = 90
Symmetry Space Group P 1 21 1
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 300 mm CCD Adjustable focusing mirrors in K-B geometry 2006-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97918 APS 23-ID-D
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 1.68 50 86.3 0.051 25.11 7 68513
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 1.68 1.74 43.6 0.496 2.426 3.9 3443
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 3D0Q 1.9 38.75 53699 2745 98.032 0.162 0.16 0.1601 0.212 0.2083 RANDOM 15.847
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] 1.171 -1.934 -1.774 0.561
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.32 r_dihedral_angle_4_deg 16.414 r_dihedral_angle_3_deg 13.578 r_scangle_it 7.825 r_dihedral_angle_1_deg 7.61 r_scbond_it 5.629 r_mcangle_it 3.006 r_mcbond_it 1.988 r_angle_refined_deg 1.416 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.32 r_dihedral_angle_4_deg 16.414 r_dihedral_angle_3_deg 13.578 r_scangle_it 7.825 r_dihedral_angle_1_deg 7.61 r_scbond_it 5.629 r_mcangle_it 3.006 r_mcbond_it 1.988 r_angle_refined_deg 1.416 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.241 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5754 Nucleic Acid Atoms Solvent Atoms 579 Heterogen Atoms 13
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection