X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details DROP: 3.0 MG/ML PROTEIN, 0.05 M IMIDAZOL MALATE BUFFER, PH 7.0, 21% PEG 400, 20 MM SRCL2, 5 MM DUDP; WELL: 0.1 M IMIDAZOLE MALATE BUFFER, PH 7.0, 42% PEG 400

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.7 α = 90
b = 106.7 β = 90
c = 106.7 γ = 90
Symmetry
Space Group P 41 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 277
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRRORS 1995-10
Diffraction Radiation
Monochromator Protocol
SI(111) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B -- 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
2.05 25 100.0 0.124 0.124 -- 10.5 -- 13598 -- -3.0 22.9
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)
2.05 2.09 100.0 0.686 0.686 3.8 10.0 --

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 2.05 20.0 -- 0.0 -- 13538 668 100.0 -- 0.168 0.167 0.201 RANDOM
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.9
Anisotropic B[1][1] 27.9
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 27.9
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 27.9
RMS Deviations
Key Refinement Restraint Deviation
p_transverse_tor 26.7
p_staggered_tor 13.4
p_planar_tor 6.1
p_xyhbond_nbd 0.15
p_multtor_nbd 0.26
p_bond_d 0.019
p_angle_d 0.04
p_planar_d 0.041
p_mcbond_it 2.9
p_mcangle_it 3.8
p_scbond_it 6.1
p_scangle_it 7.8
p_plane_restr 0.011
p_chiral_restr 0.216
p_singtor_nbd 0.19
Coordinate Error
Parameter Value
Luzzati Resolution Cutoff (Low) 20.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 919
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 80

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC Structure Refinement
Software
Software Name Purpose
REFMAC refinement
AMORE model building