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_mcangle_it 3.8
p_chiral_restr 0.216
p_bond_d 0.019
p_singtor_nbd 0.19
p_staggered_tor 13.4
p_multtor_nbd 0.26
p_transverse_tor 26.7
p_mcbond_it 2.9
p_angle_d 0.04
p_plane_restr 0.011
p_scbond_it 6.1
p_planar_tor 6.1
p_scangle_it 7.8
p_xyhbond_nbd 0.15
p_planar_d 0.041
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

Software
Software Name Purpose
AMoRE phasing
REFMAC refinement
DENZO data reduction
SCALEPACK data scaling