7K82 | pdb_00007k82

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

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
2.61	52.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.342	α = 90
b = 68.255	β = 90
c = 67.779	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	1.548600	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	2.1	40.4	99.9	0.355	0.036	0.999	18.3	97.3		14204

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	2.1	2.16	99.6		0.469	0.753	1.7	101

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	2.1	40.4	14158	590	99.944	0.193	0.1917	0.2	0.2217	0.23	38.082

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]
1.635			-0.465		-1.171

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.186
r_dihedral_angle_4_deg	22.305
r_dihedral_angle_3_deg	13.019
r_lrange_it	8.733
r_lrange_other	8.72
r_dihedral_angle_1_deg	7.287
r_scangle_it	6.325
r_scangle_other	6.322
r_mcangle_it	4.492
r_mcangle_other	4.49
r_scbond_it	4.135
r_scbond_other	4.133
r_mcbond_it	3.195
r_mcbond_other	3.189
r_angle_refined_deg	1.534
r_angle_other_deg	1.265
r_symmetry_xyhbond_nbd_refined	0.225
r_nbd_refined	0.193
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.168
r_nbd_other	0.159
r_xyhbond_nbd_refined	0.15
r_symmetry_nbd_refined	0.137
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.07
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1519
Nucleic Acid Atoms
Solvent Atoms	58
Heterogen Atoms	7

Software

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