2QDR | pdb_00002qdr

Crystal structure of a putative dioxygenase (npun_f5605) from nostoc punctiforme pcc 73102 at 2.60 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.33	293	NANODROP, 21.4% Ethanol, 0.2M Magnesium chloride, 0.1M HEPES pH 7.33, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.096	α = 90
b = 102.096	β = 90
c = 250.807	γ = 120

Symmetry
Space Group	P 62 2 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 325 mm CCD	Flat mirror (vertical focusing)	2007-04-07	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97916, 0.97883	SSRL	BL11-1

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	2.6	47.298	99.6	0.127	10.68			24629		-3	70.689

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	2.6	2.69	98.8		0.012	1.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.6	47.298	24591	1252	99.66	0.242	0.24	0.24	0.286	0.29	RANDOM	60.231

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]
2.89	1.44		2.89		-4.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.062
r_dihedral_angle_4_deg	9.89
r_dihedral_angle_3_deg	9.803
r_scangle_it	3.683
r_scbond_it	2.641
r_dihedral_angle_1_deg	2.078
r_angle_refined_deg	1.824
r_mcangle_it	1.443
r_angle_other_deg	1.235
r_mcbond_it	1
r_mcbond_other	0.264
r_xyhbond_nbd_refined	0.23
r_nbtor_refined	0.172
r_nbd_refined	0.153
r_symmetry_vdw_other	0.132
r_nbd_other	0.128
r_symmetry_hbond_refined	0.12
r_symmetry_vdw_refined	0.111
r_nbtor_other	0.08
r_chiral_restr	0.07
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4500
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
autoSHARP	phasing