3EAE | pdb_00003eae

PWWP domain of human hepatoma-derived growth factor 2 (HDGF2)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HTS	PDB Entries 2HTS and 2NLU
experimental model	PDB	2NLU	PDB Entries 2HTS and 2NLU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	2.0 M NH4SO4, 0.2 M K/Na tart, 0.1 M Na Citrate pH 5.6., VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.555	α = 90
b = 59.95	β = 90
c = 104.942	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	200	CCD	ADSC QUANTUM 315			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97940	APS	19-ID

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	2.24	40	99.7	0.084	19.947	6.9		12780

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	2.3	2.34	98.5		0.647		6.4	600

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	PDB Entries 2HTS and 2NLU	2.24	40	12780	632	96.39	0.225	0.224	0.22	0.26	0.25	RANDOM	30.079

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]
-1.26			3.56		-2.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.567
r_dihedral_angle_4_deg	20.709
r_dihedral_angle_3_deg	14.386
r_dihedral_angle_1_deg	7.081
r_scangle_it	2.379
r_scbond_it	1.68
r_angle_refined_deg	1.261
r_mcangle_it	1.009
r_mcbond_it	0.605
r_nbtor_refined	0.318
r_nbd_refined	0.2
r_symmetry_hbond_refined	0.188
r_xyhbond_nbd_refined	0.183
r_symmetry_vdw_refined	0.148
r_chiral_restr	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1322
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction