X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 303.0
Details isopropanol, strontium chloride, magnesium chloride, spermine, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 126.5 α = 90
b = 145.3 β = 90
c = 144.6 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH mirrors 2002-04-23
Diffraction Radiation
Monochromator Protocol
Si MIRRORS MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 5ID-B 0.9475,0.9293 APS 5ID-B

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
3.15 33 98.2 -- 0.076 -- 10.1 23276 23276 0.0 0.0 66.3
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)
3.15 3.24 80.9 -- 0.272 2.7 2.9 1345

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
MAD 3.15 33.0 0.0 0.0 22853 21680 1173 98.18 0.28179 0.28179 0.28043 0.30736 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 3.154 3.235 -- 66 1260 0.354 0.332 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 94.249
Anisotropic B[1][1] 4.45
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.56
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.9
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.417
r_scbond_it 1.487
r_symmetry_hbond_refined 0.174
r_symmetry_vdw_refined 0.35
r_xyhbond_nbd_refined 0.161
r_nbd_refined 0.281
r_gen_planes_refined 0.017
r_chiral_restr 0.139
r_angle_refined_deg 1.291
r_bond_refined_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.5687
Luzzati ESD (R-Free Set) 0.515
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 5802
Heterogen Atoms 35
Solvent Atoms 0

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SHARP Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
CNS refinement
SHARP model building
SCALA data reduction
XDS data collection