1XB9 | pdb_00001xb9

The structure and function of Xenopus NO38-core, a histone chaperone in the nucleolus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K5J	PDB Entry 1K5J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	296	PEG400, Tris-HCl, Calcium Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 198.913	α = 90
b = 64.549	β = 113.72
c = 97.461	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	IMAGE PLATE	RIGAKU RAXIS IV++	Mirrors	2002-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.9	90	94	0.038	0.031	14.5	4.9		89372

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.97	94		0.221	0.19	3.24	4.2	369

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB Entry 1K5J	1.9	91.29	89377	81414	6598	91.1	0.20794	0.20372	0.21	0.25504	0.26	RANDOM	25.843

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]
0.61		-0.21	-0.88		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.779
r_scangle_it	5.362
r_scbond_it	3.673
r_angle_refined_deg	2.559
r_mcangle_it	2.402
r_mcbond_it	1.574
r_angle_other_deg	1.119
r_symmetry_hbond_refined	0.656
r_symmetry_vdw_refined	0.321
r_symmetry_vdw_other	0.316
r_nbd_other	0.273
r_nbd_refined	0.205
r_xyhbond_nbd_refined	0.2
r_chiral_restr	0.183
r_nbtor_other	0.103
r_bond_refined_d	0.033
r_gen_planes_refined	0.014
r_gen_planes_other	0.013
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8032
Nucleic Acid Atoms
Solvent Atoms	305
Heterogen Atoms

Software

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