X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.8
Temperature 295.5
Details 27% PEG-MME 2000, 0.1M Tris pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.88 α = 60.96
b = 116.26 β = 77.13
c = 118.37 γ = 80.4
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2010-12-06
Diffraction Radiation
Monochromator Protocol
double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D

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 50 84.4 0.068 -- -- 2.0 -- 172551 -- -- --
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)
2.0 2.07 53.7 0.459 -- -- 1.8 --

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 2.0 49.238 -- 1.96 -- 172491 8648 84.21 -- 0.2019 0.1993 0.2495 --
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 2.0 2.0228 -- 143 3042 0.3014 0.3474 -- 47.0
X Ray Diffraction 2.0228 2.0466 -- 175 3422 0.2844 0.3324 -- 53.0
X Ray Diffraction 2.0466 2.0715 -- 195 3772 0.2693 0.3285 -- 58.0
X Ray Diffraction 2.0715 2.0977 -- 222 3904 0.2712 0.3319 -- 61.0
X Ray Diffraction 2.0977 2.1253 -- 193 4114 0.2644 0.2947 -- 63.0
X Ray Diffraction 2.1253 2.1545 -- 238 4400 0.2667 0.3239 -- 67.0
X Ray Diffraction 2.1545 2.1852 -- 245 4488 0.2614 0.3135 -- 70.0
X Ray Diffraction 2.1852 2.2179 -- 259 4760 0.2625 0.3166 -- 73.0
X Ray Diffraction 2.2179 2.2525 -- 244 4932 0.2638 0.3179 -- 76.0
X Ray Diffraction 2.2525 2.2894 -- 268 5012 0.2414 0.3393 -- 78.0
X Ray Diffraction 2.2894 2.3289 -- 281 5227 0.2466 0.3091 -- 81.0
X Ray Diffraction 2.3289 2.3713 -- 285 5460 0.2429 0.3163 -- 84.0
X Ray Diffraction 2.3713 2.4169 -- 319 5511 0.2475 0.2978 -- 85.0
X Ray Diffraction 2.4169 2.4662 -- 304 5715 0.2434 0.3081 -- 88.0
X Ray Diffraction 2.4662 2.5198 -- 314 5729 0.2405 0.3048 -- 89.0
X Ray Diffraction 2.5198 2.5784 -- 314 5964 0.2356 0.3113 -- 91.0
X Ray Diffraction 2.5784 2.6429 -- 311 5982 0.2237 0.3293 -- 93.0
X Ray Diffraction 2.6429 2.7144 -- 291 6125 0.2168 0.2856 -- 94.0
X Ray Diffraction 2.7144 2.7942 -- 330 6179 0.2199 0.2763 -- 95.0
X Ray Diffraction 2.7942 2.8844 -- 314 6221 0.22 0.2702 -- 96.0
X Ray Diffraction 2.8844 2.9875 -- 317 6299 0.2121 0.2615 -- 97.0
X Ray Diffraction 2.9875 3.1071 -- 373 6278 0.2096 0.2623 -- 98.0
X Ray Diffraction 3.1071 3.2485 -- 363 6343 0.1991 0.2587 -- 98.0
X Ray Diffraction 3.2485 3.4197 -- 360 6400 0.196 0.2357 -- 99.0
X Ray Diffraction 3.4197 3.6339 -- 316 6415 0.1832 0.2255 -- 99.0
X Ray Diffraction 3.6339 3.9144 -- 332 6438 0.1618 0.23 -- 99.0
X Ray Diffraction 3.9144 4.3081 -- 342 6395 0.1593 0.2002 -- 99.0
X Ray Diffraction 4.3081 4.931 -- 315 6455 0.1493 0.1872 -- 99.0
X Ray Diffraction 4.931 6.2105 -- 337 6439 0.176 0.2147 -- 99.0
X Ray Diffraction 6.2105 49.2528 -- 348 6422 0.1846 0.2042 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -4.5911
Anisotropic B[1][2] 2.7195
Anisotropic B[1][3] 5.305
Anisotropic B[2][2] 4.3579
Anisotropic B[2][3] 18.1828
Anisotropic B[3][3] 0.2332
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.127
f_bond_d 0.005
f_angle_d 0.918
f_chiral_restr 0.062
f_plane_restr 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 23264
Nucleic Acid Atoms 0
Heterogen Atoms 360
Solvent Atoms 1051

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing version: 2.1.4
PHENIX refinement version: 1.7_650
PDB_EXTRACT data extraction version: 3.10
Blu-Ice data collection
HKL-2000 data reduction
HKL-2000 data scaling