7CGA | pdb_00007cga

Crystal structure of human unphosphorylated p38gamma

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CM8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	291	1.9 M Sodium Malonate

Crystal Properties
Matthews coefficient	Solvent content
4.49	72.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 183.631	α = 90
b = 183.631	β = 90
c = 294.242	γ = 120

Symmetry
Space Group	P 63 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	94	CCD	RAYONIX MX300HE		2016-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL15A1	1.00	NSRRC	BL15A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	3.15	20	100	0.905	21.9	10.9		51419

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.15	3.26	100		0.86		11

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 (All)	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	1cm8	3.15	19.944	50783	2558	98.963	0.163	0.1603	0.17	0.2178	0.22	Random	65.137

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]
-0.069	-0.034		-0.069		0.224

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.315
r_dihedral_angle_3_deg	23.362
r_dihedral_angle_4_deg	22.225
r_lrange_it	13.935
r_lrange_other	13.931
r_scangle_it	9.84
r_scangle_other	9.84
r_mcangle_it	9.411
r_mcangle_other	9.41
r_dihedral_angle_1_deg	8.84
r_scbond_it	6.264
r_scbond_other	6.263
r_mcbond_it	6.054
r_mcbond_other	6.053
r_angle_refined_deg	1.739
r_angle_other_deg	1.278
r_nbd_other	0.225
r_nbd_refined	0.22
r_symmetry_nbd_other	0.199
r_symmetry_nbd_refined	0.183
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.162
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.079
r_symmetry_xyhbond_nbd_other	0.016
r_bond_refined_d	0.008
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	11192
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing