X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details 0.01M Zinc chloride, 0.1M MES, 20% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 124.67 α = 90
b = 40.98 β = 97.21
c = 52.04 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate osmic mirrors 2011-10-07
Diffraction Radiation
Monochromator Protocol
OSMIC VARIMAX SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418 -- --

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 61.84 99.9 0.086 -- -- 8.0 15360 15360 0.0 0.0 --
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 2.14 100.0 0.898 -- -- 7.9 768

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 2.1 15.0 -- 0.0 -- 15288 769 98.33 -- 0.2253 0.2236 0.2558 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 2.098 2.153 -- 60 970 0.428 0.538 -- 89.02
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 52.0382
Anisotropic B[1][1] -3.58
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.4
Anisotropic B[2][2] 1.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.34
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 28.896
r_bond_refined_d 0.006
r_mcbond_other 0.264
r_angle_refined_deg 1.183
r_dihedral_angle_3_deg 14.019
r_scbond_it 3.015
r_chiral_restr 0.049
r_gen_planes_other 0.001
r_dihedral_angle_1_deg 4.242
r_gen_planes_refined 0.004
r_scangle_it 4.277
r_dihedral_angle_4_deg 10.504
r_mcangle_it 1.91
r_mcbond_it 1.042
r_angle_other_deg 0.91
r_bond_other_d 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 909
Nucleic Acid Atoms 814
Heterogen Atoms 9
Solvent Atoms 57

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing version: 2.1.4
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
MAR345dtb data collection