X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details reservoir: 40mM MgAc/50mM NaCac pH 6.0, 20% MPD; complex solution: 50mM KCl, 10mM KH2PO4/K2HPO4 pH 7.0, 1mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.35 α = 90
b = 79.34 β = 90
c = 98.55 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2008-02-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2

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
3.04 50 100.0 -- 0.082 -- 7.3 -- 15706 -- -- --
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)
3.04 3.15 100.0 -- 0.509 4.1 6.8 --

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 3.04 15.0 -- 0.0 -- 14742 773 99.63 -- 0.23894 0.23628 0.29432 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 3.038 3.114 -- 55 1003 0.341 0.376 -- 95.49
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 72.524
Anisotropic B[1][1] 1.5
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -7.18
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.68
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.005
r_scbond_it 1.179
r_chiral_restr 0.068
r_bond_refined_d 0.008
r_dihedral_angle_2_deg 33.615
r_scangle_it 2.02
r_dihedral_angle_1_deg 5.95
r_dihedral_angle_4_deg 18.65
r_dihedral_angle_3_deg 17.357
r_mcangle_it 1.101
r_angle_refined_deg 1.112
r_mcbond_it 0.528
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4270
Nucleic Acid Atoms 278
Heterogen Atoms 20
Solvent Atoms 3

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.006
MAR345 data collection
HKL-2000 data reduction
HKL-2000 data scaling