X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.7
Details 10% SODIUM CHLORIDE W/V; PH 4.7 0.04M SODIUM ACETATE BUFFER; 80MG OF LYSOZYME PROTEIN 2ML AQUEOUS.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.64 α = 90
b = 78.64 β = 90
c = 36.45 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 (R-AXIS IV) RIGAKU OSMIC CONFOCAL MAX-FLUX 2008-12-09
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE MICROMAX 007 -- -- --

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
1.53 55.6 87.2 0.08 -- -- 6.17 -- 12866 -- 1.0 --
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)
1.53 1.58 23.2 0.29 -- 2.2 1.89 --

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
OTHER 1.8 55.64 -- -- -- 10509 556 100.0 -- 0.2 0.198 0.249 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 1.8 1.85 -- 50 740 0.288 0.381 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.91
Anisotropic B[1][1] -0.48
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.48
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.96
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.522
r_scbond_it 2.188
r_mcangle_it 1.397
r_mcbond_it 0.862
r_nbd_refined 0.202
r_gen_planes_refined 0.005
r_chiral_restr 0.104
r_dihedral_angle_4_deg 23.598
r_dihedral_angle_3_deg 14.592
r_dihedral_angle_2_deg 33.973
r_dihedral_angle_1_deg 6.137
r_angle_refined_deg 1.336
r_bond_refined_d 0.013
r_nbtor_refined 0.298
r_xyhbond_nbd_refined 0.248
r_symmetry_vdw_refined 0.186
r_symmetry_hbond_refined 0.197
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1001
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 129

Software

Computing
Computing Package Purpose
D*TREK Data Reduction (intensity integration)
D*TREK Data Reduction (data scaling)
REFMAC5 Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
REFMAC5 model building