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Human Metavinculin(residues 959-1130) in complex with PIP2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MYI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.4 294 20 mM citric acid, 80-100 mM Bis-Tris propane (pH 3.4), and 12-16% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.44 49.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.617 α = 90 b = 58.55 β = 113.15 c = 112.492 γ = 90
Symmetry Space Group C 1 2 1
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 RAYONIX MX-300 2012-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 2.75 100 99.8 0.048 0.995 16.3 8.7 19048 51.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.9 99.7 0.987 8.2 8.6
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 3MYI 2.75 50.13 19013 899 99.81 0.2092 0.2067 0.2394 0.2594 0.2789 RANDOM 53.32
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] -26.8416 -6.4221 7.2034 19.6382
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.15 t_omega_torsion 2.51 t_angle_deg 1.13 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.15 t_omega_torsion 2.51 t_angle_deg 1.13 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5177 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 74
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling MOLREP phasing