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Cerebral cavernous malformation 3 (CCM3) in complex with paxillin LD1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L8I PDB ENTRY 3L8I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1-0.2 M potassium fluoride,
15-20% PEG3350., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.28 45.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.161 α = 90 b = 117.989 β = 90 c = 123.693 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 90 CCD ADSC QUANTUM 315r mirrors 2010-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 2.8 50 99.9 0.104 0.104 17.6 7.2 -3 81.5
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) 1 2.8 2.9 100 0.86 0.86 2.5 7.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3L8I 2.8 38.92 23402 23402 1192 99.84 0.24316 0.24316 0.24034 0.29529 0.285 RANDOM 87.056
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] -2.51 0.11 2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.24 r_dihedral_angle_3_deg 20.265 r_dihedral_angle_4_deg 16.1 r_dihedral_angle_1_deg 5.354 r_scangle_it 2.745 r_mcangle_it 1.873 r_scbond_it 1.592 r_angle_refined_deg 1.316 r_mcbond_it 1.02 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.24 r_dihedral_angle_3_deg 20.265 r_dihedral_angle_4_deg 16.1 r_dihedral_angle_1_deg 5.354 r_scangle_it 2.745 r_mcangle_it 1.873 r_scbond_it 1.592 r_angle_refined_deg 1.316 r_mcbond_it 1.02 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 6351 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