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Crystal structure of CCM3, a cerebral cavernous malformation protein critical for vascular integrity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L8I THE P212121 MODEL, PDB entry 3L8I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.16 M calcium acetate, 0.08 M sodium cacodylate pH 6.5, 20% glycerol, 13.5% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.48 64.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.445 α = 90 b = 77.445 β = 90 c = 108.629 γ = 90
Symmetry Space Group P 41 2 2
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 ADSC QUANTUM 270 mirrors 2009-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.9551 NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.05 25 0.084 19.3 13.7 6769 6699 2 109
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.05 3.16 0.491 2.7 9.6 634
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 THE P212121 MODEL, PDB entry 3L8I 3.05 25 6170 316 96.56 0.27895 0.27827 0.2727 0.2926 0.2967 RANDOM 146.451
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] 5.61 5.61 -11.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.883 r_dihedral_angle_3_deg 15.178 r_dihedral_angle_4_deg 13.058 r_dihedral_angle_1_deg 3.899 r_angle_refined_deg 0.881 r_scangle_it 0.4 r_scbond_it 0.228 r_mcangle_it 0.199 r_mcbond_it 0.106 r_chiral_restr 0.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.883 r_dihedral_angle_3_deg 15.178 r_dihedral_angle_4_deg 13.058 r_dihedral_angle_1_deg 3.899 r_angle_refined_deg 0.881 r_scangle_it 0.4 r_scbond_it 0.228 r_mcangle_it 0.199 r_mcbond_it 0.106 r_chiral_restr 0.054 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 1630 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling