2APJ | pdb_00002apj

X-Ray Structure of Protein from Arabidopsis Thaliana AT4G34215 at 1.6 Angstrom Resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZMB	PHYRE SERVER HOMOLOGY MODEL BASED ON 1ZMB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
2	VAPOR DIFFUSION, HANGING DROP	5.5	277	PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.005 M BIS-TRIS, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (17% PEG 4000, 0.020 M POTASSIUM NITRATE, 0.050 M MES, 0.050 M SODIUM ACETATE PH 5.5), vapor diffusion, hanging drop, temperature 277K
1	VAPOR DIFFUSION, HANGING DROP	5.5	273	PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.005 M BIS-TRIS, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (18% PEG 4000, 0.010 M POTASSIUM NITRATE, 0.050 M MES, 0.050 M SODIUM ACETATE PH 5.5), vapor diffusion, hanging drop, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.8
2.3	46.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.688	α = 108.16
b = 71.918	β = 93.25
c = 93.213	γ = 90.4

Symmetry
Space Group	P 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	MARMOSAIC 300 mm CCD	PAIR OF BIMORPH, RHODIUM COATED KIRKPATRICK-BAEZ MIRRORS	2005-08-10	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR	2005-07-10	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.98245	APS	22-ID
2	SYNCHROTRON	APS BEAMLINE 22-ID	0.97234	APS	22-ID

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	1.6	50	94.5	0.047	17.57	3.8		125043

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	1.6	1.64	83.7	83.7	0.24	4.611	3.4

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	PHYRE SERVER HOMOLOGY MODEL BASED ON 1ZMB	1.6	35.852	124841	6226	94.39	0.147	0.14746	0.1456	0.15	0.183	0.18	RANDOM	8.471

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]
0.969	-0.051	-0.536	-0.932	-0.355	-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.928
r_dihedral_angle_4_deg	11.954
r_dihedral_angle_3_deg	11.596
r_dihedral_angle_1_deg	5.48
r_scangle_it	4.029
r_scbond_it	2.601
r_angle_refined_deg	1.617
r_mcangle_it	1.481
r_mcbond_it	0.994
r_nbtor_refined	0.31
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.193
r_symmetry_vdw_refined	0.193
r_symmetry_hbond_refined	0.184
r_chiral_restr	0.122
r_bond_refined_d	0.018
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7468
Nucleic Acid Atoms
Solvent Atoms	1611
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction