X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 297.0
Details 20 mM NaAcetate, 20% PEG 3000 + 4% PEG 600, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.87 α = 90
b = 43.87 β = 90
c = 238.31 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV mirrors 2004-05-26
Diffraction Radiation
Monochromator Protocol
Rigaku/MSC green optics SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

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
2.25 20 94.0 -- 0.044 -- 3.6 11307 11307 -- -3.0 --
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)
2.25 2.33 93.0 -- 0.439 2.1 -- --

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 2.3 19.92 -- 0.0 -- 10057 518 94.61 -- 0.23999 0.23682 0.29895 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 2.3 2.359 -- 32 673 0.328 0.561 -- 92.16
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.138
Anisotropic B[1][1] 0.14
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.28
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 2.563
r_dihedral_angle_1_deg 7.687
r_mcangle_it 1.788
r_bond_refined_d 0.018
r_dihedral_angle_3_deg 19.284
r_nbtor_refined 0.315
r_dihedral_angle_2_deg 30.013
r_dihedral_angle_4_deg 18.005
r_mcbond_it 1.015
r_angle_refined_deg 2.191
r_nbd_refined 0.252
r_symmetry_vdw_refined 0.325
r_xyhbond_nbd_refined 0.185
r_chiral_restr 0.12
r_scangle_it 3.853
r_gen_planes_refined 0.009
r_symmetry_hbond_refined 0.22
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 961
Nucleic Acid Atoms 363
Heterogen Atoms 0
Solvent Atoms 82

Software

Computing
Computing Package Purpose
CRYSTALCLEAR (MSC/RIGAKU) Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2 Structure Refinement
Software
Software Name Purpose
MOLREP model building
CrystalClear data collection
REFMAC version: 5.2 refinement