5FDJ | pdb_00005fdj

Hen egg lysozyme at room temperature solved from datasets acquired by ultrasonic acoustic levitation method and processed by CrystFEL


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XJB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5293Na acetate, MPEG 5K, NaCl, Na acetate, ethylene glycerol
Crystal Properties
Matthews coefficientSolvent content
2.0238.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.6α = 90
b = 78.6β = 90
c = 37.4γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS EIGER X 16M2015-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
11.85099.90.07415.9406.7471920911603
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)
11.81.8397.40.1310.11121.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4XJB1.839.31078256899.990.181210.179190.190.219980.23RANDOM38.145
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.295
r_dihedral_angle_3_deg14.305
r_dihedral_angle_4_deg13.818
r_long_range_B_refined8.693
r_long_range_B_other8.592
r_scangle_other7.343
r_dihedral_angle_1_deg6.757
r_scbond_it4.895
r_scbond_other4.891
r_mcangle_it3.663
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1000
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
CrystFELdata reduction
MOLREPphasing