5MID | pdb_00005mid

The study of the X-ray induced enzymatic reduction of molecular oxygen to water for laccase from Steccherinum murashkinskyi.The 14-th structure of the series with total exposition time 393 min.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MEW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	294	Protein solution (12mg/ml, 002M K-phosphate buffer, pH 6.5). Reservoir solution (0.1M citrate-phosphate buffer pH4.0, 0.2M ammonium acetat, 25% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.37	α = 90
b = 84.39	β = 90
c = 112.48	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	MAR CCD 165 mm		2009-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.81230	EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.35	67.5	98.8	0.044	0.999	20.84	3		116887		-3.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.4	99.7		0.339	0.883	3.95	3

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	5MEW	1.35	67.5	111039	5848	98.83	0.13265	0.13174	0.13	0.14991	0.15	RANDOM	11.002

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]
0.1			0.04		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.812
r_dihedral_angle_4_deg	20.375
r_dihedral_angle_3_deg	11.071
r_dihedral_angle_1_deg	7.223
r_long_range_B_refined	4.706
r_long_range_B_other	4.058
r_sphericity_bonded	3.839
r_scangle_other	2.35
r_angle_refined_deg	1.989
r_scbond_it	1.678
r_mcangle_it	1.602
r_scbond_other	1.591
r_mcangle_other	1.511
r_mcbond_it	1.078
r_mcbond_other	1.026
r_angle_other_deg	0.901
r_chiral_restr	0.134
r_bond_refined_d	0.021
r_gen_planes_refined	0.012
r_bond_other_d	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3775
Nucleic Acid Atoms
Solvent Atoms	702
Heterogen Atoms	78

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
MOLREP	phasing