X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.1
Details MICROBATCH METHOD; PROTEIN AT 45 MG/ML IN 10MM SODIUM PHOSPHATE WITH 0.25M SODIUM D-TARTRATE (PH=7.1) AND 10% (V/V) GLYCEROL; CRYSTALS GROWN AT 4 C

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.91 α = 90
b = 57.91 β = 90
c = 150.88 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
CCD ADSC CCD TOROIDAL FOCUSING MIRROR 2007-11-05
Diffraction Radiation
Monochromator Protocol
SI(111) CHANNEL CUT SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X6A -- NSLS X6A

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
1.08 20 95.6 0.04 -- -- 8.6 -- 105746 -- 2.0 --
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)
1.08 1.1 70.9 0.18 -- 8.3 5.0 --

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 1.08 19.76 -- -- -- 100419 5279 100.0 -- 0.119 0.119 0.126 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 1.08 1.11 -- 285 5495 0.108 0.128 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.76
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.04
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 2.573
r_dihedral_angle_4_deg 12.157
r_bond_refined_d 0.011
r_mcbond_it 1.368
r_scangle_it 3.428
r_dihedral_angle_2_deg 35.782
r_gen_planes_refined 0.008
r_nbtor_refined 0.311
r_symmetry_hbond_refined 0.127
r_xyhbond_nbd_refined 0.129
r_angle_refined_deg 1.524
r_chiral_restr 0.092
r_mcangle_it 2.031
r_dihedral_angle_1_deg 6.744
r_nbd_refined 0.203
r_dihedral_angle_3_deg 10.145
r_symmetry_vdw_refined 0.201
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1545
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 378

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing