X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details PEG 2000 MME, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.98 α = 90
b = 88.62 β = 90
c = 150 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 107
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ Rigaku Varimax HF 2008-03-10
Diffraction Radiation
Monochromator Protocol
Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 1.54 -- --

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
2.7 29.54 96.2 0.102 -- -- 3.45 19356 19356 -- -- 69.7
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)
2.7 2.8 85.5 0.405 -- 2.2 2.86 1705

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 2.7 28.99 -- -- 19284 19284 980 96.02 -- 0.24732 0.24267 0.33503 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 2.7 2.77 -- 57 1177 0.301 0.463 -- 84.52
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic with 8 TLS groups
Mean Isotropic B 41.289
Anisotropic B[1][1] -0.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.25
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_other 0.192
r_dihedral_angle_1_deg 5.924
r_mcangle_it 0.747
r_dihedral_angle_4_deg 14.274
r_xyhbond_nbd_refined 0.126
r_symmetry_vdw_refined 0.187
r_gen_planes_refined 0.003
r_xyhbond_nbd_other 0.004
r_bond_refined_d 0.009
r_dihedral_angle_3_deg 18.403
r_nbd_other 0.195
r_mcbond_it 0.541
r_chiral_restr 0.051
r_scbond_it 0.956
r_nbtor_other 0.084
r_mcbond_other 0.05
r_nbd_refined 0.213
r_scangle_it 1.435
r_dihedral_angle_2_deg 35.397
r_symmetry_hbond_refined 0.104
r_nbtor_refined 0.182
r_bond_other_d 0.007
r_angle_refined_deg 1.132
r_gen_planes_other 0.001
r_angle_other_deg 0.806
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5112
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 82

Software

Software
Software Name Purpose
CrystalClear data collection
PHASER phasing
REFMAC refinement version: 5.2.0019
d*TREK data reduction
d*TREK data scaling