X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 298.0
Details 0.2M ammonium phosphate, 20% PEG 3350, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 113.54 α = 90
b = 113.54 β = 90
c = 177.45 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2006-06-09
Diffraction Radiation
Monochromator Protocol
synchrotron SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 1.00000 SSRL BL11-1

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
2.5 95.78 99.87 0.117 0.117 -- 12.0 -- 39001 -- -3.0 --
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)
2.49 2.58 99.06 0.665 -- 4.4 12.0 --

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 2.5 50.0 -- -- -- 39001 2064 99.87 -- 0.2251 0.224 0.24562 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 2.495 2.56 -- 135 2815 0.301 0.32 -- 99.06
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.258
Anisotropic B[1][1] -0.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.14
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.165
r_scangle_it 3.276
r_dihedral_angle_2_deg 35.855
r_mcangle_it 1.399
r_mcbond_it 1.169
r_dihedral_angle_3_deg 16.175
r_xyhbond_nbd_refined 0.152
r_chiral_restr 0.082
r_gen_planes_refined 0.004
r_nbd_refined 0.215
r_dihedral_angle_1_deg 5.206
r_scbond_it 2.165
r_symmetry_hbond_refined 0.427
r_symmetry_vdw_refined 0.265
r_bond_refined_d 0.01
r_dihedral_angle_4_deg 17.431
r_nbtor_refined 0.312
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6509
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 173

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing