X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.5
Temperature 298.0
Details PEG8000, pH 8.5, vapor diffusion, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 122.19 α = 90
b = 79.66 β = 105.54
c = 125.91 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
CCD MARMOSAIC 225 mm CCD -- 2008-12-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.979 EMBL/DESY, Hamburg X12

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
2.1 121.3 98.4 0.085 0.085 -- 3.3 133960 133960 -- -- --
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)
2.1 2.21 94.2 0.561 0.561 1.4 3.3 18662

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 2.2 30.0 -- 0.0 -- 117344 5903 99.05 -- 0.2317 0.2281 0.3008 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 2.2 2.257 -- 428 7881 0.29 0.385 -- 95.47
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.3208
Anisotropic B[1][1] -0.37
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -2.33
Anisotropic B[2][2] 1.13
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.0
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 19.94
r_scangle_it 3.264
r_mcbond_it 0.8
r_bond_refined_d 0.014
r_angle_refined_deg 1.613
r_chiral_restr 0.105
r_dihedral_angle_2_deg 38.723
r_dihedral_angle_1_deg 7.357
r_mcangle_it 1.469
r_dihedral_angle_4_deg 23.53
r_scbond_it 2.093
r_gen_planes_refined 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 15290
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 614

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling version: 3.2.21
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
MAR345dtb data collection