X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 289.0
Details Tris-HCl, PEG4000, magnesium chloride, adenine hemisulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 37.93 α = 90
b = 75.3 β = 90
c = 78.65 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
IMAGE PLATE MARRESEARCH Mirrors 2001-10-03
Diffraction Radiation
Monochromator Protocol
Ni filter SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 -- -- --

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
1.93 54.39 99.3 0.056 0.056 -- 3.7 -- 16683 2.0 2.0 12.008
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)
1.93 2.03 99.3 0.155 0.132 5.4 3.6 2290

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 1.93 54.23 2.0 2.0 20467 16473 878 99.3 0.16011 0.16011 0.15758 0.20771 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 1.934 1.984 -- 53 1136 0.161 0.201 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.951
Anisotropic B[1][1] -1.3
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.73
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.58
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.091
r_nbd_other 0.254
r_nbd_refined 0.221
r_gen_planes_other 0.005
r_gen_planes_refined 0.009
r_chiral_restr 0.111
r_dihedral_angle_1_deg 6.055
r_angle_other_deg 0.926
r_angle_refined_deg 1.775
r_bond_other_d 0.002
r_bond_refined_d 0.021
r_xyhbond_nbd_refined 0.144
r_symmetry_vdw_refined 0.258
r_symmetry_vdw_other 0.306
r_symmetry_hbond_refined 0.173
r_mcbond_it 1.063
r_mcangle_it 1.838
r_scbond_it 3.07
r_scangle_it 4.874
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1913
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 204

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (TRUNCATE) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC Structure Refinement
Software
Software Name Purpose
REFMAC refinement
AMoRE model building
TRUNCATE data reduction
MOSFLM data collection