2WG7 | pdb_00002wg7

Structure of Oryza Sativa (Rice) PLA2

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	VAPOUR DIFFUSION, 20 DEGREES WELL CONTAINED 0.75ML OF SOLUTION A (16-18% PEG3350, 0.1M BISTRISPROPANE PH 6.5, 0.2M POTASSIUM THIOCYANATE) AND 0.25ML SOLUTION B (0.1M SODIUM ACETATE PH 4.6, 2M SODIUM CHLORIDE)

Crystal Properties
Matthews coefficient	Solvent content
2.53	50.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.667	α = 90
b = 108.667	β = 90
c = 41.652	γ = 120

Symmetry
Space Group	P 62

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			M	SINGLE WAVELENGTH
2	1	x-ray		IMAGE PLATE				M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2
2	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	27	99.7	0.08	13.91	3.4		18175		2

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	2.07	98		0.33	1.96	2.9

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	SAD	THROUGHOUT	NONE	2	27.05	18175	986	99.7	0.187	0.185	0.184	0.23	0.229	RANDOM	23.68

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]
0.55	0.28		0.55		-0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.039
r_dihedral_angle_3_deg	11.823
r_dihedral_angle_4_deg	8.951
r_dihedral_angle_1_deg	4.372
r_scangle_it	2.516
r_scbond_it	1.511
r_mcangle_it	1.104
r_angle_refined_deg	1.021
r_mcbond_it	0.568
r_nbtor_refined	0.289
r_nbd_refined	0.196
r_symmetry_vdw_refined	0.149
r_symmetry_hbond_refined	0.148
r_xyhbond_nbd_refined	0.142
r_metal_ion_refined	0.098
r_chiral_restr	0.063
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1801
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	3

Software

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