Experiment: 5M1Y

The case of 1lkr held at the PDB and its variable amino acid occupancies; re refinement of 4ow9 to correct this

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4OW9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	4.7	293	CRYSTALLIZATION CONDITIONS: 20MG HEWL CO-CRYSTALLISED WITH 1.2MG CISPLATIN WITH 75UL DMSO, 462.5UL 0.1M NAAC AND 462.5UL 1M NAI SOLUTION

Crystal Properties
Matthews coefficient	Solvent content
1.8	30

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 27.251	α = 90
b = 62.537	β = 90.92
c = 58.981	γ = 90

Symmetry
Space Group	P 1 21 1

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	APEX II CCD		2013-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER IMUS MICROFOCUS	1.5418

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	1.9	31	71	0.13	16.7	6.9		11097

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	1.9	1.97	21		0.229	2	1.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4ow9	1.904	31	1.35	11078	547	71.04	0.2182	0.2159	0.2215	0.2621

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.025
f_angle_d	0.719
f_chiral_restr	0.027
f_bond_d	0.003
f_plane_restr	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2002
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	57

Software

Software
Software Name	Purpose
PHENIX	refinement
PHASER	phasing
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling