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Crystal structure of the C2A domain of Rabphilin-3A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RSY PDB ENTRY 1RSY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 25% PEG4000, 0.1M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE, PH=4.6
Crystal Properties Matthews coefficient Solvent content 2.1 39.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.87 α = 90 b = 39.16 β = 90 c = 88.85 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 BRUKER SMART 6000 OSMIC FOCUSING MIRRORS 2005-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER ROTATING ANODE
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 1.92 44.41 97.8 0.05 19 6.13 10435 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 1.92 1.95 92.6 0.28 3 2.74
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 1RSY 1.92 44.41 9909 488 97.8 0.201 0.198 0.1885 0.269 0.1674 RANDOM 22.01
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] 1.83 0.42 -2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.67 r_dihedral_angle_3_deg 16.521 r_dihedral_angle_4_deg 14.998 r_dihedral_angle_1_deg 7.436 r_scangle_it 4.292 r_scbond_it 2.822 r_angle_refined_deg 1.752 r_mcangle_it 1.746 r_mcbond_it 1.104 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.67 r_dihedral_angle_3_deg 16.521 r_dihedral_angle_4_deg 14.998 r_dihedral_angle_1_deg 7.436 r_scangle_it 4.292 r_scbond_it 2.822 r_angle_refined_deg 1.752 r_mcangle_it 1.746 r_mcbond_it 1.104 r_nbtor_refined 0.323 r_nbd_refined 0.257 r_symmetry_hbond_refined 0.252 r_xyhbond_nbd_refined 0.201 r_symmetry_vdw_refined 0.191 r_chiral_restr 0.139 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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_refined 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1020 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing