8YGW | pdb_00008ygw

The Crystal Structure of MAPK11 from Biortus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GP0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M Bis-Tris pH6.5, 28% PEGMME2,000

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.061	α = 90
b = 61.86	β = 90
c = 147.437	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	PIXEL	DECTRIS PILATUS3 6M		2023-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.95374	CLSI	08ID-1

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	3.3	49.15	100	0.199	9.3	7.3		5815

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	3.3	3.57			0.827

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.301	49.15	5780	284	99.948	0.209	0.2054	0.21	0.2781	0.28	78.808

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]
-2.978			7.254		-4.276

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.107
r_dihedral_angle_6_deg	10.801
r_lrange_it	6.091
r_lrange_other	6.09
r_dihedral_angle_1_deg	5.281
r_mcangle_it	3.606
r_mcangle_other	3.606
r_scangle_it	2.862
r_scangle_other	2.861
r_dihedral_angle_2_deg	2.609
r_mcbond_it	2.049
r_mcbond_other	2.048
r_scbond_it	1.598
r_scbond_other	1.597
r_angle_refined_deg	0.685
r_angle_other_deg	0.239
r_nbd_refined	0.179
r_symmetry_nbd_other	0.169
r_nbtor_refined	0.168
r_nbd_other	0.157
r_xyhbond_nbd_refined	0.132
r_symmetry_nbd_refined	0.12
r_symmetry_xyhbond_nbd_refined	0.113
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.032
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2632
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing