X-RAY DIFFRACTION Experimental Data & Validation


Lost? View more X-Ray Crystallographic info.

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 70% (v/v) MPD in 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.1 α = 90
b = 81.1 β = 90
c = 223.96 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD mirror 2006-03-26
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID

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
2.5 30 93.2 0.072 -- -- 6.3 28418 28418 0.0 0.0 74.45
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)
2.5 2.59 66.8 0.298 -- 2.22 2.1 1993

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 2.501 29.116 -- 1.49 30431 28395 988 93.31 -- 0.2001 0.1979 0.2607 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 2.5006 2.6324 3050 109 3050 0.2707 0.3307 -- 74.0
X Ray Diffraction 2.6324 2.7972 4045 146 4045 0.2667 0.315 -- 98.0
X Ray Diffraction 2.7972 3.0129 4099 146 4099 0.248 0.328 -- 99.0
X Ray Diffraction 3.0129 3.3158 4123 151 4123 0.2194 0.2956 -- 100.0
X Ray Diffraction 3.3158 3.7947 4159 151 4159 0.2026 0.2685 -- 99.0
X Ray Diffraction 3.7947 4.7775 4011 146 4011 0.164 0.2458 -- 95.0
X Ray Diffraction 4.7775 29.1181 3920 139 3920 0.1922 0.2322 -- 89.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 80.2303
Anisotropic B[1][1] -0.1766
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.1766
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.3532
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.275
f_plane_restr 0.004
f_chiral_restr 0.069
f_angle_d 1.052
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3659
Nucleic Acid Atoms 1152
Heterogen Atoms 63
Solvent Atoms 70

Software

Computing
Computing Package Purpose
SERGUI Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction