X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.5
Details CRYSTALS OF NITRATE-LYSOZYME WERE GROWN UNDER A MICRO GRAVITY ENVIRONMENT DURING THE USML-2 MISSION LAUNCHED ON OCTOBER 1995 (SHUTTLE COLUMBIA). THE CRYSTALLIZATION SETUP WAS THE APCF DEVELOPPED BY EUROPEAN SPACE AGENCY. PROTEIN CONCENTRATION 10 MG/ML IN 50 MM SODIUM ACETATE BUFFER AT PH 4.5. GRADIENT CONCENTRATION APPLIED FROM 0 TO FINAL 290 MM AT 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 27.94 α = 90
b = 62.73 β = 90.76
c = 60.25 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1996-01-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON LURE BEAMLINE DW32 -- LURE DW32

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
1.45 10 95.5 0.12 -- -- 7.7 -- 35206 -- 0.0 13.7
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)
1.45 1.49 87.0 0.16 -- 4.5 3.6 --

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 1.45 6.0 -- 0.0 -- 31225 3499 95.5 -- 0.215 0.215 0.256 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 1.45 1.52 -- 403 3549 0.34 0.39 -- 87.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 16.4
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 3.7
x_scbond_it 3.21
x_mcangle_it 2.73
x_mcbond_it 2.5
x_improper_angle_d 1.14
x_bond_d 0.006
x_angle_deg 1.35
x_dihedral_angle_d 23.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Resolution Cutoff (Low) 5.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2002
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 251

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (AGROVATA, ROTAVATA) Data Reduction (data scaling)
X-PLOR 3.853 Structure Solution
X-PLOR 3.853 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.853 refinement
X-PLOR version: 3.853 model building