2NLK

Crystal structure of D1 and D2 catalytic domains of human Protein Tyrosine Phosphatase Gamma (D1+D2 PTPRG)


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 277.0
Details 10% PEG 10K, 100mM Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 118.51 α = 90
b = 134 β = 90
c = 59.08 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS -- 2006-09-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU -- -- --

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
2.4 39.94 99.5 0.099 0.099 -- 4.2 37606 37418 -- -- --
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)
2.4 2.53 98.6 0.485 0.485 1.5 3.6 5313

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 2.4 39.936 -- 0.0 37639 37345 1864 99.22 0.239 0.239 0.237 0.274 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 2.4 2.462 2680 135 2545 0.296 0.362 -- 97.6
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.159
Anisotropic B[1][1] 1.32
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.78
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.54
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.565
r_angle_other_deg 1.06
r_symmetry_vdw_refined 0.123
r_nbtor_other 0.087
r_dihedral_angle_1_deg 7.626
r_xyhbond_nbd_refined 0.16
r_dihedral_angle_3_deg 14.692
r_dihedral_angle_4_deg 20.899
r_nbd_refined 0.195
r_gen_planes_other 0.001
r_bond_other_d 0.001
r_gen_planes_refined 0.005
r_nbtor_refined 0.176
r_mcbond_other 0.132
r_dihedral_angle_2_deg 32.546
r_symmetry_hbond_refined 0.103
r_nbd_other 0.193
r_bond_refined_d 0.015
r_scangle_it 2.469
r_mcangle_it 1.066
r_chiral_restr 0.133
r_scbond_it 1.651
r_symmetry_vdw_other 0.196
r_mcbond_it 0.641
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4386
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 150

Software

Software
Software Name Purpose
SCALA data scaling
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 2.000
CrystalClear data collection version: (MSC/RIGAKU)
MOSFLM data reduction
CCP4 data scaling version: (SCALA)