4R4Z | pdb_00004r4z

Structure of PNGF-II in P21 space group

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4R4X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	289	12% PEG3350, 0.1M sodium malonate pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289 K

Crystal Properties
Matthews coefficient	Solvent content
2.62	52.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.8	α = 90
b = 94.2	β = 91.4
c = 165.8	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	196	CCD	ADSC QUANTUM 315	mirrors	2013-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	1.0000	SSRF	BL17U

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	2.8	30	91.7	0.136	9.87	2.8	60898	55844

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	82		0.42	2.28	2	6029

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	4R4X	2.81	29.5	60898	52973	2856	90.99	0.204	0.204	0.199	0.2137	0.257	0.2733	RANDOM	33.349

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]
-2.9		0.96	5.75		-2.87

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	71.818
r_dihedral_angle_2_deg	33
r_dihedral_angle_3_deg	13.745
r_sphericity_bonded	12.975
r_dihedral_angle_4_deg	11.006
r_rigid_bond_restr	8.198
r_dihedral_angle_1_deg	5.765
r_angle_other_deg	1.469
r_angle_refined_deg	1.156
r_chiral_restr	0.063
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17023
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms

Software

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