X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Details PEG 3000, NaCl, Tris HCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.99 α = 90
b = 166.01 β = 92.13
c = 74.42 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD CUSTOM-MADE -- 1999-12-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 1.0332 APS 19-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
2.14 82 97.3 0.05 -- -- 4.6 84223 84223 0.0 0.0 34.0
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)
2.14 2.22 83.3 0.205 -- 5.5 4.0 7200

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
-- 2.14 25.0 -- 0.0 84172 84172 4235 -- -- -- 0.211 0.284 --
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 2.14 2.2425 -- 485 9896 0.235 0.313 -- --
X Ray Diffraction 2.243 2.3554 -- 493 9442 0.222 0.31 -- --
X Ray Diffraction 2.355 2.4802 -- 482 8573 0.215 0.324 -- --
X Ray Diffraction 2.48 2.619 -- 412 7694 0.206 0.312 -- --
X Ray Diffraction 2.619 2.7742 -- 358 6953 0.199 0.289 -- --
X Ray Diffraction 2.774 2.949 -- 334 6185 0.197 0.291 -- --
X Ray Diffraction 2.949 3.1472 -- 296 5474 0.199 0.295 -- --
X Ray Diffraction 3.147 3.3741 -- 266 4841 0.2 0.271 -- --
X Ray Diffraction 3.374 3.6362 -- 238 4176 0.197 0.271 -- --
X Ray Diffraction 3.636 3.9425 -- 202 3587 0.196 0.236 -- --
X Ray Diffraction 3.943 4.3051 -- 155 3054 0.196 0.244 -- --
X Ray Diffraction 4.305 4.7412 -- 116 2570 0.189 0.238 -- --
X Ray Diffraction 4.741 5.2756 -- 101 2088 0.193 0.275 -- --
X Ray Diffraction 5.276 5.9458 -- 79 1691 0.227 0.323 -- --
X Ray Diffraction 5.946 6.8109 -- 76 1281 0.27 0.348 -- --
X Ray Diffraction 6.811 7.9708 -- 48 972 0.276 0.274 -- --
X Ray Diffraction 7.971 9.6068 -- 39 681 0.299 0.28 -- --
X Ray Diffraction 9.607 12.0877 -- 32 431 0.298 0.266 -- --
X Ray Diffraction 12.088 16.2961 -- 15 273 0.32 0.303 -- --
X Ray Diffraction 16.296 25.0 -- 8 75 0.412 0.287 -- --
RMS Deviations
Key Refinement Restraint Deviation
p_scangle_it 4.14
p_scbond_it 2.902
p_mcangle_it 3.874
p_mcbond_it 2.58
p_bond_d 0.015
p_angle_d 0.042
p_planar_d 0.045
p_plane_restr 0.012
p_chiral_restr 0.141
p_singtor_nbd 0.202
p_multtor_nbd 0.254
p_xyhbond_nbd 0.187
p_xhyhbond_nbd 0.304
p_planar_tor 4.357
p_staggered_tor 18.01
p_orthonormal_tor 14.79
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12360
Nucleic Acid Atoms 0
Heterogen Atoms 462
Solvent Atoms 1082

Software

Computing
Computing Package Purpose
D*TREK Data Reduction (intensity integration)
SCALEPACK, CCP4 (TRUNCATE) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC Structure Refinement
Software
Software Name Purpose
REFMAC refinement
AMoRE model building
SCALEPACK+TRUNCATE data reduction
D*Trek data collection