3PTK | pdb_00003ptk

The crystal structure of rice (Oryza sativa L.) Os4BGlu12

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	288.15	19% PEG 3350, 0.1M Tris HCl, 0.16M NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.15K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.656	α = 90
b = 112.656	β = 90
c = 182.773	γ = 90

Symmetry
Space Group	P 43 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	ADSC QUANTUM 315		2008-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.0000	NSRRC	BL13B1

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	2.49	30	99.9	0.106	6.4	10		39535

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	2.5	2.59	99.9		0.41	6.4	9.7

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 ENTRY 1CBG	2.49	30	39535	2097	99.82	0.20472	0.20245	0.2	0.24764	0.25	RANDOM	32.956

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]
1.07			1.07		-2.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.736
r_dihedral_angle_4_deg	19.477
r_dihedral_angle_3_deg	16.897
r_dihedral_angle_1_deg	5.907
r_scangle_it	2.129
r_scbond_it	1.32
r_angle_refined_deg	1.192
r_mcangle_it	0.963
r_mcbond_it	0.526
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.214
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.154
r_metal_ion_refined	0.12
r_chiral_restr	0.092
r_symmetry_hbond_refined	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7722
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	17

Software

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