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Crystal structure of Carbonic Anhydrase Nce103 from Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DDZ PDB ENTRY 1DDZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 289 20% PEG 4000, 0.2M sodium acetate, 0.1M sodium citrate, 20% ethylene glycol , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.15 42.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.57 α = 90 b = 155.73 β = 90 c = 89.69 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE MAR scanner 345 mm plate 2007-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.03 30 93.1 0.066 0.081 13.5 2.8 71916 25657
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.03 2.14 81 0.31 0.383 3.2 2.8
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 1DDZ 2.04 16.11 24369 1288 94.17 0.19912 0.19689 0.1963 0.2413 0.2407 RANDOM 21.718
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] -0.85 0.9 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.755 r_dihedral_angle_4_deg 15.433 r_dihedral_angle_3_deg 12.668 r_dihedral_angle_1_deg 5.004 r_scangle_it 2.226 r_scbond_it 1.575 r_angle_refined_deg 1.107 r_mcangle_it 0.923 r_mcbond_it 0.778 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.755 r_dihedral_angle_4_deg 15.433 r_dihedral_angle_3_deg 12.668 r_dihedral_angle_1_deg 5.004 r_scangle_it 2.226 r_scbond_it 1.575 r_angle_refined_deg 1.107 r_mcangle_it 0.923 r_mcbond_it 0.778 r_nbtor_refined 0.292 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.185 r_symmetry_hbond_refined 0.166 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.078 r_metal_ion_refined 0.031 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 3130 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 26
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling