X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Evaporation
pH 6.2
Temperature 290.0
Details 30% MPD, 80mM SrCl2, 25mM NaCl, 50mM Cacodylate equilibrated with 60%MPD, pH 6.2, EVAPORATION, temperature 290.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.29 α = 90
b = 48.73 β = 90
c = 120 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 77
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2006-03-04
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 8-BM 0.97949 APS 8-BM

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
2.32 59.98 95.9 0.108 -- -- 5.5 12751 12228 -- 0.0 59.9
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)
2.32 2.43 100.0 0.714 -- 2.4 6.9 1247

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 2.32 59.98 -- 0.0 12210 11590 598 94.92 0.26515 0.26405 0.26141 0.32037 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 2.32 2.38 1247 36 752 0.301 0.43 -- 86.03
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 51.272
Anisotropic B[1][1] -2.24
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.38
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.62
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.317
r_nbd_refined 0.165
r_scangle_it 1.94
r_angle_refined_deg 1.835
r_symmetry_vdw_refined 0.164
r_chiral_restr 0.078
r_nbtor_refined 0.279
r_bond_refined_d 0.01
r_xyhbond_nbd_refined 0.162
r_metal_ion_refined 0.222
r_gen_planes_refined 0.008
r_scbond_it 1.409
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.39
Luzzati Sigma A (Observed) 0.335
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.38
Luzzati Sigma A (R-Free Set) 0.32
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 1860
Heterogen Atoms 10
Solvent Atoms 67

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
ADSC data collection version: Quantum
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing