X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Batch Dialysis
pH 7
Details PROTEIN WAS CRYSTALLIZED BY THE BATCH DIALYSIS METHOD USING MPD AS THE PRECIPITANT AT PH 7.0, 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL)METHYL]-2 AMINOETHANESULFONATE, WITH 0.66 MM NADH AND 0.76 MM 3-BUTYLTHIOLANE 1-OXIDE. VERY CLOSE TO C-CENTERED ORTHORHOMBIC BUT SCALES VERY BADLY AS C222. SO THE SYMMETRY IS ACTUALLY P21., batch dialysis

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.93 α = 90
b = 180.2 β = 106
c = 86.8 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU MIRRORS 1995-04
Diffraction Radiation
Monochromator Protocol
NI --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH2R -- -- --

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
2.5 20 88.8 -- 0.035 -- 2.1 -- 94632 -- -- --
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)
2.5 2.54 77.2 -- 0.087 8.8 1.7 --

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
-- 2.5 20.0 -- 0.0 -- 44760 1379 88.8 -- -- 0.205 0.256 RANDOM
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.51
RMS Deviations
Key Refinement Restraint Deviation
p_special_tor 0.0
p_transverse_tor 33.5
p_staggered_tor 15.8
p_planar_tor 2.3
p_multtor_nbd 0.27
p_bond_d 0.03
p_angle_d 0.06
p_planar_d 0.06
p_mcbond_it 1.76
p_mcangle_it 2.55
p_scbond_it 2.78
p_scangle_it 4.2
p_plane_restr 0.01
p_chiral_restr 0.2
p_singtor_nbd 0.193
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11140
Nucleic Acid Atoms 0
Heterogen Atoms 216
Solvent Atoms 556

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
ARP/WARP Structure Solution
ARP/WARP, REFMAC Structure Refinement
Software
Software Name Purpose
REFMAC refinement
ARP/wARP refinement
ARP/wARP model building