X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.8
Temperature 277.0
Details 1.9M ammonium sulfate, 50mM MES, pH 5.8, vapor diffusion, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.83 α = 90
b = 61.83 β = 90
c = 111.75 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2007-07-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BSRF BEAMLINE 1W2B 1.0 BSRF 1W2B

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
2.7 50 99.6 0.134 -- -- 5.1 -- 6407 -- -- --
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)
2.7 2.8 100.0 0.531 -- -- 5.1 1147

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 2.7 15.0 -- 0.0 -- 6321 293 99.51 -- 0.238 0.234 0.307 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 2.7 2.768 -- 33 418 0.287 0.352 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.712
Anisotropic B[1][1] 0.2
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.41
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.125
r_symmetry_hbond_refined 0.245
r_dihedral_angle_2_deg 35.841
r_dihedral_angle_4_deg 23.9
r_mcangle_it 1.704
r_nbd_refined 0.26
r_scbond_it 2.272
r_angle_refined_deg 1.767
r_nbtor_refined 0.319
r_bond_refined_d 0.018
r_dihedral_angle_3_deg 21.24
r_scangle_it 3.658
r_dihedral_angle_1_deg 6.556
r_mcbond_it 0.946
r_xyhbond_nbd_refined 0.189
r_symmetry_vdw_refined 0.385
r_gen_planes_refined 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1136
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 11

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.005
HKL-2000 data collection
HKL-2000 data reduction