Experiment: 8YP8

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TG1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	295	0.1 M HEPES pH 7.8 0.6-0.8 M Sodium Citrate

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.96	α = 90
b = 81.96	β = 90
c = 122.4	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2009-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU R-AXIS IV	1.542

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.14	46.35	98	0.127	0.047	0.998	18.9	7.9		26386

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.14	2.2	80.5		0.894	0.552	0.482	1.4	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1p38	2.14	46.35	25056	1290	97.96	0.1876	0.1862	0.1927	0.2161	0.2184	RANDOM	37.56

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.34	-0.17		-0.34		1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.73
r_dihedral_angle_4_deg	16
r_dihedral_angle_3_deg	11.441
r_dihedral_angle_1_deg	6.831
r_mcangle_it	5.452
r_mcbond_other	3.583
r_mcbond_it	3.582
r_angle_refined_deg	1.476
r_angle_other_deg	1.349
r_chiral_restr	0.063

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.73
r_dihedral_angle_4_deg	16
r_dihedral_angle_3_deg	11.441
r_dihedral_angle_1_deg	6.831
r_mcangle_it	5.452
r_mcbond_other	3.583
r_mcbond_it	3.582
r_angle_refined_deg	1.476
r_angle_other_deg	1.349
r_chiral_restr	0.063
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2901
Nucleic Acid Atoms
Solvent Atoms	221
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.