3EMM | pdb_00003emm

X-ray structure of protein from Arabidopsis thaliana AT1G79260 with Bound Heme

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A13	PDB entry 2A13

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	Protein Solution (16.5 mg/mL native protein [Heme was added in purification step], 0.050 M sodium chloride, 0.0003 M TCEP, 0.005 M MES pH 6.0) mixed in a 1:1 ratio with the Well Solution (24% PEG 4K, 0.05 M BTP pH 7.0 ) Cryoprotected with 30% PEG 4K, 0.05 M BTP pH 7.0 and 15% ethylene glycol, vapor diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.4	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.749	α = 90
b = 79.732	β = 90
c = 36.971	γ = 90

Symmetry
Space Group	P 21 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	MARMOSAIC 300 mm CCD	Beryllium lenses	2008-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.358	50	97.2	0.041	22.969	4.7		37822

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)
	1.36	1.41	97.6		0.236	5.074	3.7	3728

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 2A13	1.358	47.836	37799	1864	97.155	0.171	0.17	0.21	0.198	0.24	RANDOM	15.287

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]
0.657			-0.694		0.037

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.402
r_dihedral_angle_4_deg	22.207
r_dihedral_angle_3_deg	11.129
r_dihedral_angle_1_deg	6.236
r_scangle_it	2.512
r_scbond_it	1.759
r_angle_refined_deg	1.354
r_mcangle_it	1.246
r_mcbond_it	0.769
r_nbtor_refined	0.297
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.17
r_symmetry_hbond_refined	0.119
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.089
r_bond_refined_d	0.01
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1236
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	47

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction