4QUW | pdb_00004quw

Crystal structure of the apo form of cyanobacterial aldehyde-deformylating oxygenase

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OC5	PDB ENTRY 2OC5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	0.2M Magnesium chloride hexahydrate, 0.1M Tris hydrochloride pH 8.5, 30% w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.682	α = 90
b = 61.682	β = 90
c = 110.461	γ = 90

Symmetry
Space Group	P 41 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	IMAGE PLATE	RIGAKU RAXIS IV++		2012-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E DW	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.26	50	99.7			10566	10534

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.26	2.3	99.8

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 (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 2OC5	2.26	41.15	10054	10003	505	99.49	0.22857	0.22668	0.22	0.26576	0.26	RANDOM	34.962

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]
0.93			0.93		-1.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.08
r_dihedral_angle_3_deg	16.579
r_dihedral_angle_4_deg	13.193
r_long_range_B_refined	5.944
r_long_range_B_other	5.939
r_scangle_other	4.933
r_dihedral_angle_1_deg	4.781
r_scbond_other	3.66
r_angle_other_deg	3.572
r_scbond_it	3.454
r_mcangle_other	3.287
r_mcangle_it	3.284
r_mcbond_it	2.304
r_mcbond_other	2.298
r_angle_refined_deg	1.294
r_chiral_restr	0.091
r_bond_refined_d	0.014
r_gen_planes_other	0.01
r_gen_planes_refined	0.005
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1789
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	17

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling