X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 297.0
Details 20% PEG2000, 0.3M Mg(NO3)2, 0.1M Tris, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 136.98 α = 90
b = 173.18 β = 90
c = 134.18 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2005-02-25
CCD ADSC QUANTUM 315 -- 2005-02-23
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 1.0 APS 19-ID
SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID

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
3.9 50 95.9 0.092 0.133 -- 11.4 28963 28963 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)
3.9 4.04 77.2 0.42 0.787 1.23 6.0 2304

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 3.9 20.0 -- 0.0 27320 27320 1424 97.39 0.36301 0.36301 0.36077 0.40649 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 3.9 3.997 -- 95 1682 0.516 0.548 -- 84.98
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 162.504
Anisotropic B[1][1] 11.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -19.56
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 8.54
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 0.204
r_scbond_it 0.122
r_mcangle_it 0.195
r_mcbond_it 0.108
r_nbd_refined 0.202
r_gen_planes_refined 0.002
r_chiral_restr 0.074
r_dihedral_angle_4_deg 8.164
r_dihedral_angle_3_deg 12.749
r_dihedral_angle_2_deg 26.13
r_dihedral_angle_1_deg 3.01
r_angle_refined_deg 1.172
r_bond_refined_d 0.007
r_nbtor_refined 0.306
r_xyhbond_nbd_refined 0.137
r_symmetry_vdw_refined 0.224
r_symmetry_hbond_refined 0.049
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13805
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement