3UVQ | pdb_00003uvq

Human p38 MAP Kinase in Complex with a Dibenzosuberone Derivative

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZYJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.1	293	100mM MES, 24 % PEG 4000, 50mM n-BOG, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.099	α = 90
b = 74.289	β = 90
c = 77.727	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	PIXEL	PSI PILATUS 6M	Dynamic bendable mirror	2011-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000000	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.2	49.39	99.7	0.025	33.23	5.1	20031	19971		-3	59.124

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.3	100		0.368	0.408	5.15

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1ZYJ	2.2	49.39	20031	19971	999	99.7	0.2392	0.2405	0.2364	0.2329	0.3182	0.3141	RANDOM	53.5501

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]
-0.29			-1.08		1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.466
r_dihedral_angle_3_deg	20.16
r_dihedral_angle_4_deg	18.093
r_dihedral_angle_1_deg	6.432
r_scangle_it	3.189
r_scbond_it	2.163
r_mcangle_it	1.629
r_angle_refined_deg	1.545
r_mcbond_it	0.944
r_nbtor_refined	0.312
r_symmetry_hbond_refined	0.247
r_symmetry_vdw_refined	0.236
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.179
r_chiral_restr	0.108
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2665
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	59

Software

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