7K7W | pdb_00007k7w

The X-ray crystal structure of SSR4, an S. pombe chromatin remodelling protein: native

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7K7V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		281	Crystallisation experiments were set up in SD2 sitting drop plates at 8 C with 200 nL protein plus 200 nL reservoir with 50 uL of reservoir in the wells. The protein concentration was 5 mg/mL. Reservoir conditions contained 1.5 to 1.9 M ammonium sulfate, 0.7-12% dioxane and either 100 mM MES, 100 mM bis-tris or 10% (v/v) malate-MES-tris buffer at a pH between 5.5 and 5.8

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.096	α = 90
b = 67.506	β = 90
c = 67.463	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	CCD	ADSC QUANTUM 315		2013-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.911684	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.77	47.7	100	0.169	0.047	0.998	10.9	13.5		23002

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.77	1.81	100		0.893	0.423	1.1	8

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	7k7v	1.77	47.7	22947	1090	99.97	0.178	0.1768	0.19	0.2056	0.21	21.738

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]
-0.593			1.108		-0.515

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.199
r_dihedral_angle_4_deg	15.807
r_dihedral_angle_3_deg	12.295
r_dihedral_angle_1_deg	6.862
r_lrange_it	6.19
r_lrange_other	6.134
r_scangle_it	5.088
r_scangle_other	5.086
r_scbond_it	3.309
r_scbond_other	3.308
r_mcangle_it	3.064
r_mcangle_other	3.064
r_mcbond_it	2.142
r_mcbond_other	2.128
r_angle_refined_deg	1.632
r_angle_other_deg	1.433
r_symmetry_xyhbond_nbd_refined	0.224
r_nbd_refined	0.21
r_symmetry_nbd_other	0.19
r_symmetry_nbd_refined	0.182
r_nbtor_refined	0.174
r_nbd_other	0.165
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_other	0.036
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1505
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	13

Software

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