4PWY

Crystal structure of a Calmodulin-lysine N-methyltransferase fragment


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LECFFAS03/SCWRL-modified models of PDB entries 4lec, 3bzb, 4lg1, 4mtl
experimental modelPDB 3BZBFFAS03/SCWRL-modified models of PDB entries 4lec, 3bzb, 4lg1, 4mtl
experimental modelPDB 4LG1FFAS03/SCWRL-modified models of PDB entries 4lec, 3bzb, 4lg1, 4mtl
experimental modelPDB 4MTLFFAS03/SCWRL-modified models of PDB entries 4lec, 3bzb, 4lg1, 4mtl

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.72912.0 M malonate, pH 6.7, vapor diffusion, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.564.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.935α = 90
b = 80.935β = 90
c = 121.952γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2014-01-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.9501000.107913.932722
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.931000.93913.71611

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTFFAS03/SCWRL-modified models of PDB entries 4lec, 3bzb, 4lg1, 4mtl1.92532627157399.90.16140.15990.1914RANDOM22.9872
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]
-0.05-0.050.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.521
r_dihedral_angle_4_deg19.027
r_dihedral_angle_3_deg13.412
r_dihedral_angle_1_deg6.066
r_mcangle_it3.645
r_mcbond_other2.556
r_mcbond_it2.555
r_angle_refined_deg1.518
r_angle_other_deg0.822
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.521
r_dihedral_angle_4_deg19.027
r_dihedral_angle_3_deg13.412
r_dihedral_angle_1_deg6.066
r_mcangle_it3.645
r_mcbond_other2.556
r_mcbond_it2.555
r_angle_refined_deg1.518
r_angle_other_deg0.822
r_chiral_restr0.093
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1979
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms64

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction