4NGV

Previously de-ionized HEW lysozyme batch crystallized in 0.5 M YbCl3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 193LPDB ENTRY 193L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.5293Previously de-ionized lysozyme, no buffer added, 0.5 M YbCl3, pH 4.5, Batch crystallization, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0539.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.906α = 90
b = 78.906β = 90
c = 37.699γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295IMAGE PLATEMAR scanner 345 mm plateMIRRORS2000-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLURE BEAMLINE DW32LUREDW32

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.6427.2699.80.067135.11509516.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.641.71000.2983.45.1

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 193L1.6455.792766513870118599.680.171390.170080.1861RANDOM21.731
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]
0.220.22-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.355
r_dihedral_angle_3_deg15.65
r_dihedral_angle_4_deg9.561
r_dihedral_angle_1_deg5.393
r_scbond_it3.771
r_mcangle_it1.855
r_mcbond_it1.221
r_mcbond_other1.22
r_angle_refined_deg1.049
r_angle_other_deg0.763
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.355
r_dihedral_angle_3_deg15.65
r_dihedral_angle_4_deg9.561
r_dihedral_angle_1_deg5.393
r_scbond_it3.771
r_mcangle_it1.855
r_mcbond_it1.221
r_mcbond_other1.22
r_angle_refined_deg1.049
r_angle_other_deg0.763
r_chiral_restr0.066
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
TRUNCATEdata scaling
HKL-2000data collection