X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.5
Details CHICKEN EGG WHITE LYSOZYME (FLUKA) HAS BEEN DISSOLVED IN 50 MM SODIUM ACETATE BUFFER PH 4.57 AND CRYSTALLIZED BY SITTING DROP DIFFUSION METHOD. EACH DROP CONTAINED 20 MG/ML OF LYSOZYME AND 5.5 PERCENT OF NACL IN 25 MM OF NA[AC] PH 4.57

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.35 α = 90
b = 78.35 β = 90
c = 36.9 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 63
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD (QUANTUM 315R) ADSC -- 2011-11-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 -- SOLEIL PROXIMA 1

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
1.5 39.17 99.6 0.06 -- -- 6.35 -- 20915 -- -3.0 24.394
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)
1.5 1.51 100.0 0.6 -- 3.19 6.38 --

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
ISOMORPHOUS REPLACEMENT 1.5 39.17 -- -- -- 17978 947 100.0 -- 0.16971 0.16755 0.21094 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 1.5 1.539 -- 70 1314 0.229 0.301 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.991
Anisotropic B[1][1] 0.15
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.15
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.3
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.153
r_scbond_it 3.347
r_mcangle_it 2.131
r_mcbond_it 1.325
r_gen_planes_refined 0.013
r_chiral_restr 0.157
r_dihedral_angle_4_deg 20.255
r_dihedral_angle_3_deg 15.827
r_dihedral_angle_2_deg 35.722
r_dihedral_angle_1_deg 6.21
r_angle_refined_deg 2.161
r_bond_refined_d 0.024
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1001
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 171

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
REFMAC Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
REFMAC model building