4NGZ

Previously de-ionized HEW lysozyme crystallized in 0.5 M YbCl3/30% (v/v) glycerol and collected at 125K


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, 30% (v/v) glycerol , pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9938.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.589α = 90
b = 78.589β = 90
c = 37.017γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray125IMAGE PLATERIGAKU RAXIS IIC2000-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
11.719.6599.70.06723.39.41324220.1
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)
11.71.7697.70.2023.84.4

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 193L1.755.572187211957124199.510.180810.178240.20515RANDOM21.581
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]
0.510.51-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.818
r_dihedral_angle_4_deg17.71
r_dihedral_angle_3_deg13.763
r_dihedral_angle_1_deg5.379
r_scbond_it3.38
r_mcangle_it1.907
r_mcbond_it1.374
r_mcbond_other1.318
r_angle_refined_deg1.296
r_angle_other_deg0.861
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.818
r_dihedral_angle_4_deg17.71
r_dihedral_angle_3_deg13.763
r_dihedral_angle_1_deg5.379
r_scbond_it3.38
r_mcangle_it1.907
r_mcbond_it1.374
r_mcbond_other1.318
r_angle_refined_deg1.296
r_angle_other_deg0.861
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms129
Heterogen Atoms6

Software

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