X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details 20 mg/mL Protein, 25% PEG 3350, 0.2M Ammonium sulfate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.59 α = 90
b = 38.1 β = 101.72
c = 76.03 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 2006-06-15
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT -- -- --

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
1.65 26.49 95.8 0.031 -- -- 6.8 -- 35314 -- -- --
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)
1.65 1.7 64.5 0.134 -- 12.5 6.4 --

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 1.65 26.49 -- 0.0 -- 35314 1801 96.64 -- 0.17 0.169 0.196 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 1.65 1.693 -- 94 1853 0.279 0.259 -- 73.53
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.354
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_angle_refined_deg 1.134
r_scbond_it 1.641
r_bond_refined_d 0.008
r_dihedral_angle_1_deg 5.144
r_gen_planes_other 0.002
r_symmetry_hbond_refined 0.294
r_mcbond_it 0.89
r_mcangle_it 1.01
r_nbtor_refined 0.172
r_nbtor_other 0.08
r_symmetry_vdw_other 0.231
r_dihedral_angle_3_deg 11.64
r_dihedral_angle_4_deg 14.398
r_chiral_restr 0.071
r_symmetry_vdw_refined 0.172
r_bond_other_d 0.001
r_scangle_it 2.38
r_gen_planes_refined 0.004
r_nbd_refined 0.213
r_dihedral_angle_2_deg 30.383
r_mcbond_other 0.148
r_nbd_other 0.18
r_angle_other_deg 0.838
r_xyhbond_nbd_refined 0.229
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2387
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 304

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.000
SBC-Collect data collection
HKL-2000 data reduction
HKL-2000 data scaling