3AEQ

Structure of the light-independent protochlorophyllide reductase catalyzing a key reduction for greening in the dark

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	16% PEG4000, 0.2M SODIUM/POTASSIUM PHOSPHATE(PH5.0), pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.632	α = 90
b = 81.278	β = 100.43
c = 177.103	γ = 90

Symmetry
Space Group	P 1 21 1

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		2007-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A		Photon Factory	BL-5A

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	2.9	50	92	0.106				46513		-2	73.23

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2ZMP	2.9	47.25	42703	2167	88.2	0.238	0.235	0.298	RANDOM	49.91

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]
-0.24		1.08	1.79		-1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.521
r_dihedral_angle_3_deg	20.83
r_dihedral_angle_4_deg	17.701
r_dihedral_angle_1_deg	5.699
r_scangle_it	1.655
r_angle_refined_deg	1.347
r_scbond_it	0.952
r_mcangle_it	0.647
r_mcbond_it	0.354
r_nbtor_refined	0.308
r_nbd_refined	0.221
r_symmetry_vdw_refined	0.212
r_xyhbond_nbd_refined	0.136
r_metal_ion_refined	0.099
r_chiral_restr	0.084
r_symmetry_hbond_refined	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12740
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	106

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling