X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 289.0
Details 0.2 M Sodium acetate, 0.1 m Bis-tris-propane, 20% w/v PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.32 α = 90
b = 61.55 β = 90
c = 113.69 γ = 90
Symmetry
Space Group P 2 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR ADSC QUANTUM 210 -- 2008-07-30
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1

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 50 94.6 0.085 -- -- 4.6 17823 17823 -3.0 -3.0 31.238
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 2.2 96.6 0.478 -- 4.11 -- 10623

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 50.0 -- 0.0 17823 17823 913 94.58 -- 0.1602 0.1572 0.2187 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 2.1 2.154 1262 68 1262 0.202 0.295 -- 97.29
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.61
Anisotropic B[1][1] -1.16
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.46
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.3
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.538
r_scbond_it 2.603
r_mcangle_it 1.735
r_mcbond_it 1.003
r_gen_planes_refined 0.01
r_chiral_restr 0.124
r_dihedral_angle_4_deg 17.531
r_dihedral_angle_3_deg 15.266
r_dihedral_angle_2_deg 35.414
r_dihedral_angle_1_deg 5.286
r_angle_refined_deg 2.282
r_bond_refined_d 0.022
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1243
Nucleic Acid Atoms 773
Heterogen Atoms 0
Solvent Atoms 296

Software

Computing
Computing Package Purpose
MXCuBE Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
Phaser version: 1.3.3 molecular replacement
Xscale data reduction