3IW6 | pdb_00003iw6

Human p38 MAP Kinase in Complex with a Benzylpiperazin-Pyrrol

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	100mM MES, 20-30% PEG 4000, 50mM n-BOG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70	α = 90
b = 68.74	β = 90
c = 74	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	CCD	MARRESEARCH	Dynamically bendable mirror	2009-05-01	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	2.1	45	99.1	0.091	17.88	4.02	21461	21265		-3	26.761

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.2	99.8		0.445	5.5	4.06	2758

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 (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	PDB ENTRY 1zyj	2.1	40.89	21461	21265	851	100	0.213	0.21	0.21	0.273	0.27	RANDOM	20.738

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]
0.4			-0.51		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.238
r_dihedral_angle_3_deg	18.001
r_dihedral_angle_4_deg	17.275
r_dihedral_angle_1_deg	6.188
r_scangle_it	3.867
r_scbond_it	2.455
r_mcangle_it	1.727
r_angle_refined_deg	1.638
r_mcbond_it	1.008
r_nbtor_refined	0.314
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.18
r_symmetry_vdw_refined	0.161
r_symmetry_hbond_refined	0.112
r_chiral_restr	0.109
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2727
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	89

Software

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