3Q3U | pdb_00003q3u

Trametes cervina lignin peroxidase

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FM4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	30% MPD, 10% PEG 4000, 0.1M Imidazole-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.904	α = 90
b = 72.931	β = 90
c = 95.232	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 315r		2010-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9763	ESRF	ID29

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	1.85	43.9	96.6	0.075	24.1	4.9		26056	2	2	10.502

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	1.85	1.95	77.2		0.216	9.1	3.2	2947

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	3FM4	1.85	43.9	25492	24651	1314	96.61	0.16	0.1511	0.14874	0.1516	0.19564	0.1461	RANDOM	11.986

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]
0.27			0.38		-0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.226
r_dihedral_angle_4_deg	22.838
r_dihedral_angle_3_deg	13.645
r_dihedral_angle_1_deg	6.118
r_scangle_it	3.93
r_scbond_it	2.702
r_angle_refined_deg	1.839
r_mcangle_it	1.621
r_mcbond_it	1.109
r_chiral_restr	0.145
r_bond_refined_d	0.025
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2461
Nucleic Acid Atoms
Solvent Atoms	343
Heterogen Atoms	55

Software

Software
Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling