2ZB0 | pdb_00002zb0

Crystal structure of P38 in complex with biphenyl amide inhibitor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.378	α = 90
b = 85.716	β = 90
c = 124.661	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++	mirrors	2000-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH2R	1.5418

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	35	95.9	0.076	12.9			28080			33.218

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	2.1	2.18	91.1		0.465	2.8		2615

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	2.1	20	27981	1403	100	0.174	0.172	0.18	0.212	0.21	RANDOM	41.498

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]
-1.43			0.06		1.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.293
r_dihedral_angle_4_deg	18.813
r_dihedral_angle_3_deg	14.632
r_dihedral_angle_1_deg	5.776
r_scangle_it	4.249
r_scbond_it	2.982
r_mcangle_it	2.089
r_angle_refined_deg	1.46
r_mcbond_it	1.324
r_nbtor_refined	0.307
r_nbd_refined	0.211
r_symmetry_hbond_refined	0.195
r_xyhbond_nbd_refined	0.168
r_symmetry_vdw_refined	0.164
r_chiral_restr	0.095
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2810
Nucleic Acid Atoms
Solvent Atoms	285
Heterogen Atoms	36

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction