2XRZ | pdb_00002xrz

X-ray structure of archaeal class II CPD photolyase from Methanosarcina mazei in complex with intact CPD-lesion

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		STRUCTURAL DATA OF NATIVE M. MAZEI PHOTOLYASE.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6		0.2 M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE PH 4.6, 10% (W/V) PEG 4000, 10% (V/V) GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
2.73	59.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.7	α = 90
b = 116.2	β = 90
c = 168.3	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 CCD		2008-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	2.2	29.48	99.9	0.08	17.5	4.9		72130		-3	35.6

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	2.2	2.32	100		0.69	2.6	4.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	STRUCTURAL DATA OF NATIVE M. MAZEI PHOTOLYASE.	2.2	29.48	70962	1094	99.94	0.17093	0.17036	0.18	0.20819	0.22	SHELLS	47.114

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]
0.4			-1.36		0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.28
r_dihedral_angle_4_deg	15.683
r_dihedral_angle_3_deg	13.769
r_dihedral_angle_1_deg	5.37
r_scangle_it	2.177
r_scbond_it	1.389
r_angle_refined_deg	1.363
r_angle_other_deg	0.952
r_mcangle_it	0.887
r_mcbond_it	0.46
r_mcbond_other	0.113
r_chiral_restr	0.071
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	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
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7125
Nucleic Acid Atoms	1017
Solvent Atoms	635
Heterogen Atoms	153

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing