X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Counter Diffusion in Modified Apcf Reactors
pH 4.5
Temperature 293.0
Details CRYSTALLISATION TOOK PLACE IN THE EUROPEAN SPACE AGENCY (ESA) ADVANCED PROTEIN CRYSTALLISATION FACILITY (APCF) ONBOARD THE NASA SPACE SHUTTLE'S STS-95 MISSION. A NEW APCF REACTOR WITH A LONG PROTEIN CHAMBER (67 MM) WAS DESIGNED TO PERFORM CRYSTALLIZATION USING THE COUNTER-DIFFUSION METHOD UNDER MICROGRAVITY CONDITIONS. THE PROTEIN CHAMBER WAS FILLED WITH A SOLUTION OF 99 MG/ML OF HEN EGG WHITE LYSOZYME (SUPPLIED BY SEIKAGAKU, BATCH NUMBER 100940, LOT E96302) DISSOLVED IN 0.05 M ACETATE BUFFER (PH 4.5). THE SALT CHAMBER CONTAINED 20% W/V NACL AND 0.05 M ACETATE BUFFER (PH 4.5). THE ROTATORY PLUG CONNECTING THE PROTEIN AND THE SALT CHAMBERS WAS FILLED WITH 10% W/V NACL, 0.5% W/V AGAROSE GEL AND 0.05 M ACETATE BUFFER. CRYSTALLISATION TOOK PLACE IN MICROGRAVITY AT 20+/-0.1 C., Counter-Diffusion in modified APCF reactors, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.06 α = 90
b = 77.06 β = 90
c = 37.22 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
2 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1998-12-10
IMAGE PLATE MARRESEARCH -- 1998-12-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.9057 EMBL/DESY, HAMBURG X11
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8337 EMBL/DESY, HAMBURG BW7B

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
0.94 31 98.9 0.052 -- -- 5.5 402070 72390 0.0 -3.0 8.7
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)
0.94 0.96 88.6 0.329 -- 2.6 -- 3912

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 0.94 31.0 -3.0 0.0 72390 72390 3655 98.9 0.1226 0.1226 0.1233 0.1509 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 0.94 0.96 3912 -- -- 0.3 -- -- 88.6
X Ray Diffraction 0.96 0.97 2052 -- -- 0.222 -- -- 100.0
X Ray Diffraction 0.97 0.99 3918 -- -- 0.184 -- -- 100.0
X Ray Diffraction 0.99 1.01 3594 -- -- 0.167 -- -- 99.9
X Ray Diffraction 1.01 1.03 3332 -- -- 0.15 -- -- 100.0
X Ray Diffraction 1.03 31.0 55582 -- -- 0.118 -- -- 99.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ANISOTROPIC
Mean Isotropic B 14.4
RMS Deviations
Key Refinement Restraint Deviation
s_approx_iso_adps 0.072
s_similar_adp_cmpnt 0.048
s_rigid_bond_adp_cmpnt 0.006
s_anti_bump_dis_restr 0.067
s_similar_dist 0.0
s_non_zero_chiral_vol 0.115
s_zero_chiral_vol 0.104
s_from_restr_planes 0.031
s_angle_d 0.037
s_bond_d 0.016
Coordinate Error
Parameter Value
Number Disordered Residues 37.0
Occupancy Sum Hydrogen 956.3
Occupancy Sum Non Hydrogen 1173.6
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1001
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 233

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
SHELXL-97 Structure Refinement
Software
Software Name Purpose
SHELXL-97 refinement
CNS model building
SCALEPACK data reduction
DENZO data collection