X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 277.0
Details PEG 4000, Magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.71 α = 90
b = 42.71 β = 90
c = 229.47 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2010-05-02
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.100 NSLS X25

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
2.3 42.72 97.2 0.08 -- -- 4.7 16713 16713 3.0 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)
2.301 2.35 100.0 0.222 -- -- 5.0 933

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 2.301 42.72 -- 0.0 16713 16713 896 97.05 -- 0.2069 0.2042 0.258 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 2.301 2.36 -- 55 1243 0.207 0.248 -- 97.08
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.0525
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.026
r_scbond_it 1.316
r_mcangle_it 1.01
r_mcbond_it 0.602
r_symmetry_hbond_refined 0.119
r_bond_refined_d 0.009
r_angle_refined_deg 1.273
r_dihedral_angle_1_deg 6.765
r_dihedral_angle_2_deg 34.596
r_dihedral_angle_3_deg 14.957
r_dihedral_angle_4_deg 19.198
r_chiral_restr 0.08
r_gen_planes_refined 0.004
r_nbd_refined 0.195
r_nbtor_refined 0.303
r_xyhbond_nbd_refined 0.13
r_symmetry_vdw_refined 0.178
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3692
Nucleic Acid Atoms 0
Heterogen Atoms 154
Solvent Atoms 73

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 version: 5.2.0019 refinement
Phaser molecular replacement
SCALEPACK data scaling