6VNA | pdb_00006vna

Pden_1323

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	ITasser		itasser

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	glycerol, PEG 4000, sodium acetate, Tris

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.843	α = 90
b = 117.044	β = 99.376
c = 59.382	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	PIXEL	DECTRIS EIGER X 16M		2018-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.0332	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.2	61.25	99.7	0.997	7.3	2		32977

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.27			0.582

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	itasser	2.2	58.657	24814	1294	99.595	0.214	0.2115	0.22	0.2587	0.26	64.131

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]
-2.995		-3.54	-3.766		7.519

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.869
r_dihedral_angle_3_deg	15.759
r_dihedral_angle_4_deg	14.546
r_lrange_other	11.327
r_lrange_it	11.323
r_scangle_it	8.347
r_scangle_other	8.346
r_dihedral_angle_1_deg	7.998
r_mcangle_other	7.389
r_mcangle_it	7.388
r_scbond_it	5.32
r_scbond_other	5.319
r_mcbond_it	5.053
r_mcbond_other	5.046
r_angle_other_deg	2.346
r_angle_refined_deg	1.516
r_nbd_other	0.219
r_symmetry_nbd_other	0.216
r_nbd_refined	0.203
r_symmetry_xyhbond_nbd_refined	0.165
r_xyhbond_nbd_refined	0.146
r_nbtor_refined	0.143
r_symmetry_nbd_refined	0.072
r_symmetry_nbtor_other	0.071
r_chiral_restr	0.059
r_bond_other_d	0.035
r_symmetry_xyhbond_nbd_other	0.035
r_bond_refined_d	0.007
r_gen_planes_other	0.007
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3150
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms

Software

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