X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 291.0
Details ammonium sulfate 1.5M, sodium cacodylate 0.1M, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 135.5 α = 90
b = 135.5 β = 90
c = 94.86 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 283
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2001-05-25
Diffraction Radiation
Monochromator Protocol
Si (1 1 1) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON LURE BEAMLINE DW32 0.9485 LURE DW32

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
1.85 30 99.2 0.064 -- -- 6.1 -- 75048 0.0 2.5 25.4
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)
1.85 1.95 95.2 0.286 -- 2.6 5.5 10357

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 1.85 30.0 0.0 0.0 -- 70264 4719 99.1 0.164 0.155 0.147 0.164 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 1.85 1.97 11920 734 -- 0.185 0.176 0.007 95.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 17.3
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.022
r_xyhbond_nbd_refined 0.142
r_scbond_it 2.804
r_symmetry_vdw_refined 0.14
r_dihedral_angle_2_deg 16.057
r_mcangle_it 3.092
r_nbd_refined 0.25
r_symmetry_hbond_refined 0.082
r_angle_refined_deg 1.753
r_scangle_it 4.399
r_mcbond_it 1.926
r_chiral_restr 0.144
r_dihedral_angle_1_deg 4.497
r_gen_planes_refined 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.16
Luzzati Sigma A (Observed) 0.08
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.16
Luzzati Sigma A (R-Free Set) 0.07
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4049
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 315

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
AMoRE phasing
REFMAC refinement version: 5.0
CCP4 data scaling version: (SCALA)