3S7E | pdb_00003s7e

Crystal structure of Ara h 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EA7	PDB ENTRY 2EA7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	15% PEG400, 100 mM NaCl, Na citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.368	α = 90
b = 93.368	β = 90
c = 237.111	γ = 120

Symmetry
Space Group	H 3

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	RIGAKU SATURN 92	mirrors (VariMax)	2011-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5718

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	2.7	50	92.1	0.053	0.053	18.5	3.1	19169	19169		-3	34.1

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	2.7	2.75	64.8		0.159	0.159	6.6	3.1	680

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	PDB ENTRY 2EA7	2.71	25.69	15974	15974	834	80.21	0.2376	0.2376	0.23646	0.24	0.25968	0.26	RANDOM	24.248

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]
-4.62			-4.62		9.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.77
r_dihedral_angle_4_deg	19.807
r_dihedral_angle_3_deg	17.701
r_dihedral_angle_1_deg	7.034
r_angle_other_deg	4.299
r_angle_refined_deg	1.328
r_scangle_it	1.136
r_mcangle_it	0.836
r_scbond_it	0.659
r_mcbond_it	0.541
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	5676
Nucleic Acid Atoms
Solvent Atoms	28
Heterogen Atoms	2

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
REFMAC	refinement
Coot	model building
CCP4	refinement
HKL-2000	data reduction
HKL-2000	data scaling