3QHB

Crystal structure of oxidized Symerythrin from Cyanophora paradoxa

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	5.5	279	PEG3350, NH4Cl, BisTris, pH 5.5, hanging drop, temperature 279K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.593	α = 90
b = 81.593	β = 90
c = 46.277	γ = 120

Symmetry
Space Group	P 32

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 Q315R		2010-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.976	ALS	5.0.1

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	1.2	30.6	100	0.079	0.079	23.4	17.8	107444	107444

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	1.2	1.25	100		0.335	0.335	6.3	10.7

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1RYT	1.2	30.6	107444	102004	5397	99.92	0.10188	0.10067	0.12453	RANDOM	10.462

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]
0.05	0.03		0.05		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.679
r_sphericity_free	22.754
r_dihedral_angle_4_deg	18.676
r_dihedral_angle_3_deg	13.698
r_scangle_it	11.749
r_sphericity_bonded	9.835
r_scbond_it	8.787
r_mcangle_it	5.52
r_dihedral_angle_1_deg	5.304
r_rigid_bond_restr	4.412
r_mcbond_it	4.199
r_angle_refined_deg	3.625
r_angle_other_deg	3.014
r_mcbond_other	2.005
r_chiral_restr	0.272
r_gen_planes_refined	0.021
r_bond_refined_d	0.019
r_gen_planes_other	0.012
r_bond_other_d	0.001
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2756
Nucleic Acid Atoms
Solvent Atoms	555
Heterogen Atoms	4

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
PHENIX	phasing