X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 289.0
Details 0.2 M di-Ammonium citrate pH 5.0, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.46 α = 90
b = 80.48 β = 90
c = 83.61 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2013-03-09
Diffraction Radiation
Monochromator Protocol
Si 111 channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-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
1.15 32.47 98.0 0.068 0.068 -- 7.7 121117 121117 0.0 -3.0 11.6
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)
1.15 1.17 82.3 0.628 0.628 2.0 3.9 5028

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
SAD 1.15 32.47 -- 0.0 114953 114953 6058 97.85 0.12173 0.12173 0.12008 0.15257 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 1.15 1.18 7027 377 7027 0.238 0.284 -- 82.09
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.885
Anisotropic B[1][1] 0.6
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.12
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.983
r_dihedral_angle_2_deg 33.585
r_sphericity_free 31.075
r_dihedral_angle_3_deg 12.568
r_dihedral_angle_1_deg 6.129
r_rigid_bond_restr 8.034
r_gen_planes_other 0.004
r_gen_planes_refined 0.011
r_bond_refined_d 0.018
r_angle_other_deg 1.099
r_dihedral_angle_4_deg 16.674
r_chiral_restr 0.111
r_sphericity_bonded 14.319
r_bond_other_d 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2833
Nucleic Acid Atoms 0
Heterogen Atoms 65
Solvent Atoms 669

Software

Software
Software Name Purpose
HKL-3000 data collection
HKL-3000 phasing version: SOLVE/RESOLVE
SHELXD phasing
SHELXE model building
MLPHARE phasing
DM model building
ARP/wARP model building
REFMAC refinement version: 5.7.0029
Coot model building
HKL-3000 data reduction
HKL-3000 data scaling
DM phasing