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Crystal structure of CALX-CBD1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DPK pdb entry 2DPK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 291 50 mM MES, 20% PEG 3350, pH 6.0, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.29 46.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.372 α = 90 b = 73.722 β = 90 c = 129.713 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 MARMOSAIC 225 mm CCD 2005-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.90682 SLS X06SA
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 2.25 19.6 94.4 0.072 26203
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 2.25 2.3 71.8 0.544 3.1 6.3 1259
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 2DPK 2.25 19.59 24832 1341 94.5 0.21279 0.20973 0.2663 0.26933 0.3103 RANDOM 48.676
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] -1.54 4.62 -3.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.984 r_dihedral_angle_4_deg 26.083 r_dihedral_angle_3_deg 19.992 r_dihedral_angle_1_deg 9.171 r_scangle_it 3.047 r_scbond_it 2.182 r_angle_refined_deg 1.955 r_mcangle_it 1.217 r_mcbond_it 0.72 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.984 r_dihedral_angle_4_deg 26.083 r_dihedral_angle_3_deg 19.992 r_dihedral_angle_1_deg 9.171 r_scangle_it 3.047 r_scbond_it 2.182 r_angle_refined_deg 1.955 r_mcangle_it 1.217 r_mcbond_it 0.72 r_nbtor_refined 0.318 r_symmetry_vdw_refined 0.27 r_nbd_refined 0.243 r_xyhbond_nbd_refined 0.191 r_symmetry_hbond_refined 0.167 r_metal_ion_refined 0.157 r_chiral_restr 0.139 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3576 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 22
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling