3WU8 | pdb_00003wu8

Spatiotemporal development of soaked protein crystal; derivative 1080 sec

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH METHOD	4.5	293	25mg/ml Lysozyme, 0.05M SODIUM ACETATE, 0.7M SODIUM CHLORIDE, pH 4.5, BATCH METHOD, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.206	α = 90
b = 79.206	β = 90
c = 37.858	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	300	CCD	MARMOSAIC 225 mm CCD		2013-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1.07345	SPring-8	BL26B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	50	99.6	0.082	22.8	6.9	8599	8563		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03	99.8		0.268	5.1	7	404

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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2LYM	2	50	8567	8541	402	99.7	0.17167	0.17167	0.16959	0.1697	0.21639	0.2171	RANDOM	19.909

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]
-0.21			-0.21		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.285
r_dihedral_angle_4_deg	21.358
r_dihedral_angle_3_deg	16.475
r_long_range_B_refined	7.212
r_dihedral_angle_1_deg	6.202
r_scbond_it	3.114
r_mcangle_it	2.568
r_mcbond_it	1.615
r_angle_refined_deg	1.572
r_chiral_restr	0.118
r_bond_refined_d	0.013
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	4

Software

Software
Software Name	Purpose
BSS	data collection
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling