X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 291.0
Details 18% PEG8000, 0.2M magnesium acetate, 0.1M sodium cacodylate, pH 6.5, vapor diffusion, sitting drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.53 α = 90
b = 67.53 β = 90
c = 179.96 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 -- 2006-10-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E 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
2.2 30 100.0 0.119 -- -- 6.2 -- 40474 -- -- --
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)
2.2 2.28 -- 0.976 -- -- 6.0 --

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 2.2 20.0 -- -- -- 21799 1033 99.177 0.216 -- 0.2135 0.2693 thin shells
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 2.2 2.256 -- 0 1592 0.239 -- -- 99.687
X Ray Diffraction 2.256 2.317 -- 218 1301 0.246 0.344 -- 99.541
X Ray Diffraction 2.317 2.384 -- 0 1464 0.245 -- -- 99.389
X Ray Diffraction 2.384 2.456 -- 0 1451 0.243 -- -- 99.657
X Ray Diffraction 2.456 2.535 -- 181 1215 0.223 0.264 -- 99.359
X Ray Diffraction 2.535 2.623 -- 0 1362 0.227 -- -- 99.634
X Ray Diffraction 2.623 2.72 -- 156 1158 0.243 0.339 -- 98.723
X Ray Diffraction 2.72 2.829 -- 0 1269 0.236 -- -- 98.755
X Ray Diffraction 2.829 2.952 -- 0 1212 0.23 -- -- 99.101
X Ray Diffraction 2.952 3.093 -- 117 1057 0.224 0.294 -- 98.49
X Ray Diffraction 3.093 3.256 -- 0 1103 0.226 -- -- 99.013
X Ray Diffraction 3.256 3.447 -- 96 972 0.203 0.275 -- 98.981
X Ray Diffraction 3.447 3.678 -- 0 1001 0.211 -- -- 98.621
X Ray Diffraction 3.678 3.961 -- 76 865 0.192 0.266 -- 99.053
X Ray Diffraction 3.961 4.322 -- 68 800 0.192 0.229 -- 97.748
X Ray Diffraction 4.322 4.804 -- 0 808 0.168 -- -- 98.657
X Ray Diffraction 4.804 5.495 -- 45 680 0.191 0.19 -- 99.725
X Ray Diffraction 5.495 6.607 -- 32 608 0.245 0.296 -- 100.0
X Ray Diffraction 6.607 8.872 -- 21 504 0.211 0.284 -- 99.81
X Ray Diffraction 8.872 20.0 -- 23 344 0.221 0.229 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.089
Anisotropic B[1][1] 1.466
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.466
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.932
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.079
r_nbtor_refined 0.172
r_nbtor_other 0.087
r_gen_planes_other 0.001
r_bond_other_d 0.002
r_symmetry_vdw_refined 0.117
r_nbd_refined 0.198
r_dihedral_angle_4_deg 19.032
r_dihedral_angle_2_deg 39.851
r_mcbond_it 2.456
r_bond_refined_d 0.016
r_angle_other_deg 0.907
r_gen_planes_refined 0.004
r_dihedral_angle_1_deg 6.431
r_nbd_other 0.193
r_dihedral_angle_3_deg 15.358
r_xyhbond_nbd_refined 0.147
r_scangle_it 3.256
r_symmetry_vdw_other 0.299
r_mcbond_other 0.653
r_symmetry_hbond_refined 0.179
r_scbond_it 2.394
r_mcangle_it 3.663
r_angle_refined_deg 1.409
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2538
Nucleic Acid Atoms 0
Heterogen Atoms 63
Solvent Atoms 75

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement version: refmac_5.2.0019
PDB_EXTRACT data extraction version: 1.701
ARP/wARP model building
Coot model building
MolProbity model building