3AJG | pdb_00003ajg

Crystal structure of PcyA V225D-biliverdin IX alpha complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D1E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	293	0.8-1.0M NaH2PO4, 1.0-1.2M K2HPO4, 100mM sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.046	α = 90
b = 74.875	β = 90
c = 84.169	γ = 90

Symmetry
Space Group	P 21 21 21

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 QUANTUM 315		2009-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0000	SPring-8	BL41XU

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	1.9	50	98.5	0.08	16.9	6.8	36692	36692

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)
	1.9	1.97	99.6		0.37		6.7	3623

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 (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	2D1E	1.9	32.88	34843	34843	1842	98.31	0.2316	0.23403	0.23081	0.25	0.29483	0.31	RANDOM	36.837

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]
-0.01			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.707
r_dihedral_angle_3_deg	18.492
r_dihedral_angle_4_deg	17.672
r_dihedral_angle_1_deg	7.829
r_scangle_it	4.23
r_scbond_it	2.868
r_angle_refined_deg	2.281
r_mcangle_it	2.045
r_mcbond_it	1.346
r_angle_other_deg	0.672
r_symmetry_vdw_refined	0.352
r_nbtor_refined	0.312
r_nbtor_other	0.289
r_nbd_other	0.258
r_nbd_refined	0.24
r_mcbond_other	0.194
r_xyhbond_nbd_refined	0.177
r_symmetry_hbond_refined	0.172
r_chiral_restr	0.137
r_bond_refined_d	0.019
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3810
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement