3MYL

Insights into the Importance of Hydrogen Bonding in the Gamma-Phosphate Binding Pocket of Myosin: Structural and Functional Studies of Ser236


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VOMpdb entry 1VOM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP827712.5% MePEG5K, 117mM ammonium acetate, 100mM Hepps, 2mM MgCl2, 2mM sodium pyrophosphate , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.9257.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.045α = 90
b = 180.779β = 90
c = 53.89γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2008-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID1.00707APS19-ID

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
123099.80.1150.11517.67.7690556905519.7
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)RedundancyNumber Unique Reflections (All)
22.0798.60.4060.4063.97.86769

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1VOM229.696905565472348398.710.187570.187570.184560.24378RANDOM22.093
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]
0.40.34-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.369
r_dihedral_angle_4_deg17.446
r_dihedral_angle_3_deg16.437
r_dihedral_angle_1_deg6.772
r_scangle_it5.084
r_scbond_it3.403
r_mcangle_it2.152
r_angle_refined_deg1.958
r_mcbond_it1.271
r_chiral_restr0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.369
r_dihedral_angle_4_deg17.446
r_dihedral_angle_3_deg16.437
r_dihedral_angle_1_deg6.772
r_scangle_it5.084
r_scbond_it3.403
r_mcangle_it2.152
r_angle_refined_deg1.958
r_mcbond_it1.271
r_chiral_restr0.16
r_bond_refined_d0.026
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5917
Nucleic Acid Atoms
Solvent Atoms736
Heterogen Atoms10

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling