X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 289.0
Details 1.4M Sodium Malonate, 0.1M Bis-Tris Propane:NaOH, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.01 α = 90
b = 76.01 β = 90
c = 161.26 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirror 2012-04-16
Diffraction Radiation
Monochromator Protocol
Si 111 Crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97915 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
2.15 33.5 99.8 0.122 -- -- 9.2 26537 26537 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)
2.15 2.19 100.0 0.604 -- 4.6 9.3 1275

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 2.148 33.262 -- 1.34 26457 26457 1335 99.56 0.1648 0.1648 0.1624 0.2087 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 2.1482 2.225 -- 116 2403 0.1889 0.2325 -- 97.0
X Ray Diffraction 2.225 2.3141 -- 138 2457 0.1881 0.2747 -- 100.0
X Ray Diffraction 2.3141 2.4194 -- 118 2473 0.1714 0.2363 -- 100.0
X Ray Diffraction 2.4194 2.5469 -- 128 2519 0.1744 0.2105 -- 100.0
X Ray Diffraction 2.5469 2.7064 -- 135 2475 0.1807 0.2369 -- 100.0
X Ray Diffraction 2.7064 2.9152 -- 144 2499 0.1933 0.3006 -- 100.0
X Ray Diffraction 2.9152 3.2084 -- 146 2487 0.1936 0.2613 -- 100.0
X Ray Diffraction 3.2084 3.6721 -- 146 2508 0.1622 0.2131 -- 100.0
X Ray Diffraction 3.6721 4.6245 -- 131 2566 0.1263 0.1459 -- 99.0
X Ray Diffraction 4.6245 33.2662 -- 133 2735 0.1522 0.1749 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -7.7538
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -7.7538
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 15.5075
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.066
f_dihedral_angle_d 13.685
f_angle_d 1.04
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3027
Nucleic Acid Atoms 0
Heterogen Atoms 38
Solvent Atoms 191

Software

Computing
Computing Package Purpose
sbc-collect Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
SHELXD/MLPHARE/DM/ARP/wARP/HKL3000 Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
SHELXD/MLPHARE/DM/ARP/wARP/HKL3000 model building
sbc-collect data collection