X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 3.8
Temperature 318.0
Details Protein Solution: 20mg/ml lysozyme,50mM sodium acetate, 150mM NaCl, Reservoir Solution: 50mM sodium acetate, 1-1.5M NaCl, 2.5% benzyl alcohol, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 318K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.2 α = 90
b = 78.2 β = 90
c = 37.17 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate Mirrors 2012-08-16
Diffraction Radiation
Monochromator Protocol
Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418 -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.88 50 99.7 0.038 0.038 -- 8.8 9843 9843 2.0 2.0 27.83
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.88 1.91 100.0 0.16352 0.169 0.169 8.5 475

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.88 34.971 2.0 1.34 9843 9812 471 99.73 -- 0.1851 0.1831 0.2245 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.88 2.152 -- 165 3027 0.1923 0.2409 -- 100.0
X Ray Diffraction 2.152 2.7111 -- 144 3094 0.1703 0.2284 -- 100.0
X Ray Diffraction 2.7111 34.9772 -- 162 3220 0.1862 0.2189 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 27.83
Anisotropic B[1][1] 1.7494
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.7494
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.4988
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.007
f_angle_d 1.072
f_plane_restr 0.003
f_chiral_restr 0.081
f_dihedral_angle_d 13.565
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1001
Nucleic Acid Atoms 0
Heterogen Atoms 27
Solvent Atoms 67

Software

Software
Software Name Purpose
HKL-2000 data collection
MLPHARE phasing
PHENIX refinement version: (phenix.refine: 1.7.2_869)
HKL-2000 data reduction
HKL-2000 data scaling