8CX3 | pdb_00008cx3

Crystal structure of full-length mesothelin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7UED	PDB entry 7UED

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.2	289	0.9-1.1 M sodium/potassium phosphate, pH 8.2

Crystal Properties
Matthews coefficient	Solvent content
9.05	86.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 197.171	α = 90
b = 279.324	β = 125.091
c = 170.046	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2010-08-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	0.89197	APS	22-BM

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	3.6	50	91.4	0.123	4.87	2.5		78378

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	3.6	3.73	78.1		0.48

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entry 7UED	3.609	49.292	77988	3948	91.046	0.292	0.2908	0.27	0.3105	0.29	128.434

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]
-6.781		13.9	2.742		4.039

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.252
r_dihedral_angle_6_deg	9.595
r_dihedral_angle_2_deg	7.916
r_dihedral_angle_1_deg	4.687
r_lrange_it	1.93
r_lrange_other	1.93
r_mcangle_it	0.843
r_mcangle_other	0.843
r_angle_refined_deg	0.797
r_scangle_it	0.523
r_scangle_other	0.523
r_mcbond_it	0.457
r_mcbond_other	0.457
r_scbond_it	0.278
r_scbond_other	0.278
r_angle_other_deg	0.264
r_nbd_refined	0.191
r_symmetry_nbd_other	0.18
r_symmetry_nbd_refined	0.171
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.145
r_nbd_other	0.141
r_symmetry_nbtor_other	0.073
r_symmetry_xyhbond_nbd_refined	0.073
r_chiral_restr	0.038
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11757
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	203

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing