3HJ2 | pdb_00003hj2

Crystal structure of covalent dimer of HNP1

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	0.1 M Na-citrate (pH 5.6), 0.2 M NH4-acetate, 30% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.07	α = 90
b = 49.37	β = 90
c = 24.99	γ = 90

Symmetry
Space Group	P 21 21 2

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	Rosenbaum-Rock monochromator high-resolution double-crystal Si(220)	2007-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

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	1.4	24.68	96.3	0.065	0.065	22.5	6.2	11611	11611	-1.7	-3	22.2

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)
	1.4	1.45	100		0.114	0.114	17.8	6.4	1171

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 (All)	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	1dfn	1.4	15	10987	10987	579	96.44	0.20059	0.20059	0.19886	0.267	0.23578	0.3023	RANDOM	25.827

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]
-0.32			-0.39		0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.594
r_dihedral_angle_3_deg	13.398
r_dihedral_angle_4_deg	12.451
r_sphericity_free	10.232
r_dihedral_angle_1_deg	7.617
r_sphericity_bonded	5.154
r_scangle_it	4.558
r_scbond_it	3.512
r_mcangle_it	2.893
r_mcbond_it	2.108
r_rigid_bond_restr	1.994
r_angle_refined_deg	1.857
r_chiral_restr	0.136
r_bond_refined_d	0.02
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	487
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling