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Crystal structure of the c2a domain of rabphilin-3a in complex with a calcium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CHD PDB entry 2CHD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 10 mM CaCl2, 150mM NaCl, 25mM HEPES ph 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.69 α = 90 b = 40.03 β = 90 c = 90.25 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 298 IMAGE PLATE MAR scanner 345 mm plate mirrors 2012-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5417
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 2.5 40 72.3 0.143 3.6 2.4 3660 2 2
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 2.5 2.64 68.3 0.515 1.9 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2CHD 2.5 40 2 3490 164 70.15 0.24531 0.24318 0.2462 0.28943 0.2871 RANDOM 45.055
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] 0.86 0.37 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.597 r_dihedral_angle_3_deg 14.538 r_dihedral_angle_4_deg 11.574 r_dihedral_angle_1_deg 5.812 r_long_range_B_refined 2.199 r_long_range_B_other 2.198 r_angle_refined_deg 0.934 r_mcangle_it 0.798 r_mcangle_other 0.798 r_angle_other_deg 0.643
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.597 r_dihedral_angle_3_deg 14.538 r_dihedral_angle_4_deg 11.574 r_dihedral_angle_1_deg 5.812 r_long_range_B_refined 2.199 r_long_range_B_other 2.198 r_angle_refined_deg 0.934 r_mcangle_it 0.798 r_mcangle_other 0.798 r_angle_other_deg 0.643 r_scangle_other 0.63 r_mcbond_it 0.433 r_mcbond_other 0.433 r_scbond_it 0.342 r_scbond_other 0.341 r_chiral_restr 0.055 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1019 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 1
Software Software Software Name Purpose MAR345dtb data collection REFMAC refinement MOSFLM data reduction SCALA data scaling