3RIN | pdb_00003rin

p38 kinase crystal structure in complex with small molecule inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	22% PEG3350, 0.2 M sodium chloride, 1 mM THP, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.11	α = 90
b = 86.62	β = 90
c = 123.48	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	100	IMAGE PLATE	RIGAKU RAXIS IV++		2006-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

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	19.79	93.3	0.08		2.97	25286	20902

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)
1	2.2	2.28	96.1		0.41		3.03

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	PDB ENTRY 1OVE	2.2	19.78	20902	1081	82.66	0.2649	0.2614	0.25	0.3082	0.31	RANDOM	39.6547

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]
0.15			-0.19		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.368
r_dihedral_angle_4_deg	25.979
r_dihedral_angle_3_deg	17.111
r_dihedral_angle_1_deg	7.199
r_scangle_it	3.735
r_scbond_it	2.488
r_angle_refined_deg	1.91
r_mcangle_it	1.661
r_mcbond_it	1.006
r_nbtor_refined	0.309
r_nbd_refined	0.229
r_symmetry_vdw_refined	0.206
r_symmetry_hbond_refined	0.164
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.116
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2807
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling
MOLREP	phasing