5YK4 | pdb_00005yk4

Mismatch Repair Protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E3M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	300	10-14% (W/V) PEG 4000, 0.1-0.2M MGCL2, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.94	α = 90
b = 102.4	β = 90
c = 236.17	γ = 90

Symmetry
Space Group	P 21 2 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	CCD	MARMOSAIC 225 mm CCD		2014-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.9537	ESRF	BM14

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	2.97	50	98.7	0.064	8.6	3.5		43285

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	2.97	3.05	99.2		0.56	2	3.6

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	1E3M	2.97	50	43285	2301	99.4	0.247	0.246	0.25	0.269	0.27	RANDOM	99.33

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]
3.63			0.57		-4.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.634
r_dihedral_angle_3_deg	18.812
r_long_range_B_refined	14.263
r_dihedral_angle_4_deg	11.601
r_mcangle_it	7.4
r_dihedral_angle_1_deg	6.147
r_scbond_it	4.89
r_mcbond_it	4.524
r_angle_refined_deg	1.084
r_chiral_restr	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11810
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	54

Software

Software
Software Name	Purpose
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement