1YN9 | pdb_00001yn9

Crystal structure of baculovirus RNA 5'-phosphatase complexed with phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I9T	PDB entry 1I9T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	295	sodium/potassium phosphate, sodium acetate, guanidine hydrochloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.8	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.91	α = 90
b = 74.13	β = 92.38
c = 105.2	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	100	CCD	MARRESEARCH		2003-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	0.9479	APS	5ID-B

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	1.5	150	97.1	0.073	0.066	6.8	4.4	424098	97263			14.4

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)
	1.5	1.54	90.4		0.302	0.25	2.7	2.8	6308

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-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 1I9T	1.5	105.41	92370	4870	96.84	0.167	0.16702	0.1656	0.17	0.19427	0.2	RANDOM	14.41

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]
-0.69		-0.38	-0.23		0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.878
r_dihedral_angle_4_deg	13.302
r_dihedral_angle_3_deg	11.962
r_dihedral_angle_1_deg	5.567
r_scangle_it	2.945
r_scbond_it	2.044
r_angle_refined_deg	1.233
r_mcangle_it	1.202
r_mcbond_it	1.082
r_angle_other_deg	0.779
r_symmetry_vdw_other	0.295
r_nbd_refined	0.22
r_nbtor_refined	0.183
r_nbd_other	0.182
r_mcbond_other	0.18
r_symmetry_vdw_refined	0.148
r_xyhbond_nbd_refined	0.136
r_symmetry_hbond_refined	0.136
r_nbtor_other	0.082
r_chiral_restr	0.069
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4120
Nucleic Acid Atoms
Solvent Atoms	597
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
CCP4	data scaling
AMoRE	phasing