X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.4
Temperature 298.0
Details Crystals of hen egg white lysozyme (HEWL)-Pt compound adducts appeared in solutions consisting of 1.1 M NaCl, 0.1 M sodium acetate pH 4.4. Single crystals suitable for X-ray experiments were grown by the hanging drop vapor-diffusion method using a 1:1 ratio of reservoir solution and protein adducts solution with a protein concentration of about 15 mg x ml.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.41 α = 90
b = 77.41 β = 90
c = 37.35 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
CCD RIGAKU SATURN 944 -- 2015-12-01
Diffraction Radiation
Monochromator Protocol
-- --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE ENRAF-NONIUS FR571 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
1.75 54.74 93.7 0.04 -- -- 6.8 -- 11233 -- -- --
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)
1.75 1.78 70.7 0.22 -- -- 3.1 --

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 1.75 54.74 -- -- -- 10646 556 93.8 -- 0.161 0.158 0.211 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 1.75 1.8 -- 28 598 0.221 0.304 -- 71.38
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.61
Anisotropic B[1][1] 0.37
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.37
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.73
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 2.69
r_mcbond_other 2.031
r_long_range_B_refined 5.905
r_mcangle_other 2.698
r_dihedral_angle_4_deg 17.729
r_scangle_other 4.447
r_scbond_other 3.119
r_scbond_it 3.121
r_dihedral_angle_3_deg 13.227
r_long_range_B_other 5.91
r_chiral_restr 0.135
r_gen_planes_other 0.003
r_dihedral_angle_2_deg 37.637
r_mcbond_it 2.044
r_dihedral_angle_1_deg 6.757
r_angle_refined_deg 1.92
r_bond_refined_d 0.02
r_gen_planes_refined 0.011
r_bond_other_d 0.002
r_angle_other_deg 1.186
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1001
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 138

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0135
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing