1LZ9 | pdb_00001lz9

ANOMALOUS SIGNAL OF SOLVENT BROMINES USED FOR PHASING OF LYSOZYME

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8LYZ	PDB ENTRY 8LYZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6		CRYSTALLIZED IN HANGING DROPS. 15 MG/ML PROTEIN SOLUTION IN 100 MM SODIUM ACETATE PH 4.6 AND 1 M SODIUM BROMIDE.

Crystal Properties
Matthews coefficient	Solvent content
2.05	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.6	α = 90
b = 78.6	β = 90
c = 37.2	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	100	IMAGE PLATE	MARRESEARCH	BENT MIRROR	1998-05-07	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9B	0.9188, 0.9195, 0.9198, 0.9201	NSLS	X9B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.7	20	99	0.035	0.035	50.2	8.5		13429			16.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.73	80		0.182	0.182	10	7

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	FREE R	PDB ENTRY 8LYZ	1.7	20	13309	1318	99	0.21	0.21	0.21	0.29	0.28	RANDOM 10 %	17.3

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]
0.644			0.644		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	17.6
p_staggered_tor	14.9
p_scangle_it	6.86
p_planar_tor	6.6
p_scbond_it	5.71
p_mcangle_it	3.69
p_mcbond_it	3.11
p_multtor_nbd	0.299
p_chiral_restr	0.264
p_xyhbond_nbd	0.254
p_singtor_nbd	0.178
p_angle_d	0.053
p_planar_d	0.053
p_bond_d	0.032
p_plane_restr	0.021
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1010
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	7

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CCP4	model building
REFMAC	refinement
CCP4	phasing