3DKE

Polar and non-polar cavities in phage T4 lysozyme


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.92772.0-2.2 M NaH2PO4 and K2HPO4, pH 6.9, 5mM BME, 5mM oxidized BME, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthew coefficientSolvent content
2.754.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.226α = 90
b = 60.226β = 90
c = 96.677γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-01-25MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.10.9796,0.9797,0.9742,0.9807ALS8.2.1

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
11.2552.299.90.11523.29.656299211.6
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)
11.251.271000.21413.97.12753

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.2552.1353423285199.810.156260.155380.17281RANDOM14.834
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]
-0.6-0.3-0.60.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.99
r_dihedral_angle_4_deg12.38
r_dihedral_angle_3_deg9.729
r_dihedral_angle_1_deg4.551
r_scangle_it3.414
r_scbond_it2.393
r_mcangle_it1.152
r_angle_refined_deg1.142
r_mcbond_it0.671
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.99
r_dihedral_angle_4_deg12.38
r_dihedral_angle_3_deg9.729
r_dihedral_angle_1_deg4.551
r_scangle_it3.414
r_scbond_it2.393
r_mcangle_it1.152
r_angle_refined_deg1.142
r_mcbond_it0.671
r_nbtor_refined0.306
r_nbd_refined0.202
r_symmetry_vdw_refined0.196
r_symmetry_hbond_refined0.188
r_xyhbond_nbd_refined0.121
r_chiral_restr0.069
r_metal_ion_refined0.052
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_metal_ion_other
r_nbd_other
r_symmetry_vdw_other
r_angle_other_deg
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbtor_other
r_mcbond_other
r_gen_planes_other
r_bond_other_d
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1305
Nucleic Acid Atoms
Solvent Atoms256
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing